Compositions and methods for treatment of skin disorders

ABSTRACT

Described herein are compositions and methods of treatment for acne and other skin disorders involving the use of probiotics. In certain aspects, microbes included in the probiotics have been engineered or selected for the treatment of specific skin disorders.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims priority to U.S. Provisional Ser. Nos.62/325,851 filed on Apr. 21, 2016; 62/368,829 filed on Jul. 29, 2016;62/368,837 filed on Jul. 29, 2016; 62/385,831 filed on Sep. 9, 2016; and62/441,931 filed on Jan. 3, 2017 all of which are incorporated herein intheir entirety.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has been filedelectronically in ASCII format and is hereby incorporated by referencein its entirety. Said ASCII copy, created on Apr. 20, 2017, is named48236-706_201_SL.txt and is 2,294,816 bytes in size.

BACKGROUND OF THE INVENTION

The community of microorganisms living on and/or within an individual isthe microbiome. The microbiome consists of many different bacterialspecies some of which are beneficial, neutral or deleterious to humanhealth. Alterations in the microbiome have been connected to manydisease states such as inflammatory diseases, metabolic disease,developmental diseases, psychological diseases and cancer. Determiningthe composition of the microbiome, and altering the microbiome from apathological to healthy state holds great therapeutic promise for manydifferent diseases.

SUMMARY

Provided herein are microbiome-based approaches to skin therapy usingbeneficial bacteria on the skin to eliminate or reduce harmful bacteriaand restore skin to a healthy state. The methods and compositionsdisclosed herein may be used for a wide range of skin disordersincluding acne, eczema, psoriasis, rosacea and seborrheic dermatitis.Problems with current treatments for these disorders include antibioticresistance, side effects, complicated regimens, and lack of long-termeffectiveness. Treatments disclosed herein may provide alternatives toantibiotics, use healthy bacteria, present few side effects, with simpletreatment regimens and long-term effectiveness.

Compositions described herein generally contain at least onehealth-associated microbe or probiotic that conveys beneficial effectsto a subject with a skin disorder. Thus, the compositions disclosedherein are effective on the skin (e.g., at skin temperature). Thesecompositions sometimes contain a mixture of several strains that haveeach been isolated, purified, selected or engineered to provide aspecific cocktail of bacteria that does not occur in nature. Thesestrains can be stored or packaged with a preservative agent, such asglycerol or polyethylene glycol in a container or on an applicator suchas a cotton swab, as shown in FIG. 1. These containers and applicatorscan be stored in a freezer, refrigerator or on a shelf at roomtemperature, both before and during use.

Many of the compositions and methods disclosed herein comprise bacteriaknown as Propionibacterium acnes, abbreviated P. acnes, and usesthereof, respectively. However, other bacteria, including geneticallymodified strains, and uses thereof are also contemplated herein. Somestrains of P. acnes used in compositions and methods disclosed hereinare referred to herein as healthy strains of P. acnes or, forsimplicity, “healthy P. acnes.” Healthy strains of P. acnes generallypromote skin health by preventing a skin disorder or reducing symptomsof a skin disorder. Healthy strains of P. acnes may even promote skinhealth by eliminating the cause of a skin disorder. Other strains of P.acnes are referred to herein as pathogenic strains or “pathogenic P.acnes.” Pathogenic P. acnes generally promote or cause a skin disorderor symptoms thereof. Generally, pathogenic P. acnes are not used incompositions and methods described herein. Instead, methods andcompositions disclosed herein may be useful in reducing or preventinggrowth of pathogenic P. acnes on the skin of a subject. In some cases,an amount of P. acnes can be considered healthy or pathogenic, too muchor too little being desirable or undesirable. In some cases, acombination of multiple P. acnes strains confers health. Conversely, insome cases, a different combination of multiple P. acnes strains can bepathogenic. Strains of P. acnes, combinations thereof, and amountsthereof that are healthy and pathogenic are described herein.

Compositions and methods disclosed herein may comprise bacteria with agiven genetic signature and uses thereof, respectively. While P. acnesis the bacteria primarily exemplified herein, it is contemplated thatother bacteria having a particular genetic signature that is similar tohealthy P. acnes could likewise be useful for compositions and methodsdisclosed herein. For example, many P. acnes strains that are identifiedas healthy herein comprise a combination of a deoxyribose operonrepressor (deoR), a type II lipase, and a CRISPR associated Casendonuclease. Additionally, healthy P. acnes strains are generallyassociated with an absence or only small amounts of an extrachromosomalplasmid known in the art as pIMPLE plasmids. It has previously beenreported that some strains of P. acnes harbor an extrachromosomalplasmid, given the term, “pIMPLE plasmid,” by those in the field. Suchplasmids are readily found in the art. pIMPLE plasmids may have multipleopen reading frames (ORFs). The presence of these aforementioned genes(e.g., deoR, lipase, Cas) and/or a low presence of pIMPLE plasmid mayprovide a healthy skin promoting genetic signature that can be used toidentify bacteria other than P. acnes that are useful in compositionsand methods of treating acnes described herein.

In some aspects, disclosed herein are pharmaceutical compositions thatcomprise: a first therapeutically effective amount of a firsthealth-associated Propionibacterium microbe, wherein the firsthealth-associated Propionibacterium microbe produces less than about onemicromolar porphyrin; a second therapeutically effective amount of asecond health-associated microbe; and a pharmaceutically acceptableexcipient or biological stabilizer. In some embodiments, the secondhealth-associated microbe comprises a strain of Propionibacterium. Insome embodiments, the second health-associated microbe produces lessthan about one micromolar porphyrin. In some embodiments, the firsthealth-associated Propionibacterium microbe and the secondhealth-associated Propionibacterium microbe collectively produce lessthan about one micromolar porphyrin. In some embodiments, at least oneof the first health-associated Propionibacterium microbe and the secondhealth-associated Propionibacterium microbe produce less than about 200nM porphyrin. In some embodiments, at least one of the firsthealth-associated Propionibacterium microbe and the secondhealth-associated Propionibacterium microbe produce less than about 100nM porphyrin. In some embodiments, the first health-associatedPropionibacterium microbe and the second health-associatedPropionibacterium microbe collectively produce less than about 100 nMporphyrin. In some embodiments, at least one of the firsthealth-associated Propionibacterium microbe and the secondhealth-associated Propionibacterium microbe produce less than about onemicromolar porphyrin in situ. In some embodiments, at least one of thefirst health-associated Propionibacterium microbe and the secondhealth-associated Propionibacterium microbe produce less than about onemicromolar porphyrin in vitro. In some embodiments, at least the firsthealth-associated Propionibacterium microbe comprises a strain ofPropionibacterium acnes, Propionibacterium granulosum, Propionibacteriumavidum, or Propionibacterium acnes subsp. defendens. In someembodiments, at least the first health-associated Propionibacteriummicrobe comprises a strain of Propionibacterium acnes. In someembodiments, at least the first health-associated Propionibacteriummicrobe comprises a Propionibacterium acnes of a ribotype RT1 or RT2. Insome embodiments, at least the first health-associated Propionibacteriummicrobe: (a) comprises at least one gene encoding an ATP bindingcassette transporter; (b) comprises at least one gene encoding at leastone of a deoxyribose operon repressor and a type II lipase, and lessthan about 10% pIMPLE plasmid; or (c) lacks at least one gene encoding aDNA binding response regulator or a phosphoglycerate kinase.

In some aspects, disclosed herein are pharmaceutical compositions thatcomprise: (a) a therapeutically effective amount of a health-associatedPropionibacterium acnes microbe, wherein the health-associatedPropionibacterium acnes microbe is characterized by at least one of thefollowing: comprises at least one gene encoding at least one of adeoxyribose operon repressor and a type II lipase, and less than about10% pIMPLE plasmid; comprises at least one gene encoding an ATP bindingcassette transporter; or lacks at least one gene encoding a DNA bindingresponse regulator or a phosphoglycerate kinase, and (b) apharmaceutically acceptable excipient or biological stabilizer. In someembodiments, the health-associated Propionibacterium acnes microbe hasbeen engineered or selected to comprise a deoxyribose operon repressorand a type II lipase. In some embodiments, a Cas5 protein is absent fromthe health-associated Propionibacterium acnes microbe. In someembodiments, the health-associated Propionibacterium acnes microbeexpresses an ATP binding cassette transporter. In some embodiments, thehealth-associated Propionibacterium acnes microbe does not express a DNAbinding response regulator or a phosphoglycerate kinase. In someembodiments, the health-associated Propionibacterium acnes microbecomprises an RT1 or RT2 ribotype. In some embodiments, thehealth-associated Propionibacterium acnes microbe does not comprise anRT6 ribotype. In some embodiments, the health-associatedPropionibacterium acnes microbe comprises a mixture of two or moredifferent ribotypes of Propionibacterium acnes. In some embodiments, thehealth-associated Propionibacterium acnes microbe comprises an HP3A11strain, an HP3B4 strain, an HP4G1 strain, or an HP5G4 strain. In someembodiments, the pharmaceutical probiotic composition comprises anadditional strain of bacteria, wherein the additional strain comprisesPropionibacterium avidum or Propionibacterium granulosum. In someembodiments, the additional strain comprises Propionibacterium acnessubsp. defendens.

In some aspects, disclosed herein are methods of treating a skindisorder or condition comprising applying a therapeutically effectiveamount of a pharmaceutical probiotic composition comprising: (a) atherapeutically effective amount of a health-associatedPropionibacterium acnes microbe, wherein the health-associatedPropionibacterium acnes microbe is characterized by at least one of thefollowing: comprises at least one gene encoding at least one of adeoxyribose operon repressor and a type II lipase, and less than about10% pIMPLE plasmid; comprises at least one gene encoding an ATP bindingcassette transporter; or lacks at least one gene encoding a DNA bindingresponse regulator or a phosphoglycerate kinase, and (b) apharmaceutically acceptable excipient or biological stabilizer. In someembodiments, the skin disorder or condition comprises acne, eczema,seborrheic dermatitis, psoriasis, or rosacea, or a combination thereof.In some embodiments, the health-associated Propionibacterium acnesmicrobe has been engineered or selected to at least one gene encodingthe deoxyribose operon repressor and the type II lipase. In someembodiments, a Cas5 protein is absent from the health-associatedPropionibacterium acnes microbe. In some embodiments, thehealth-associated Propionibacterium acnes microbe comprises an RT1 orRT2 ribotype. In some embodiments, the health-associatedPropionibacterium acnes microbe does not comprise an RT6 ribotype. Insome embodiments, the health-associated Propionibacterium acnes microbecomprises a mixture of two or more different ribotypes. In someembodiments, the health-associated Propionibacterium acnes microbecomprises an HP3A11 strain, an HP3B4 strain, an HP4G1 strain, or anHP5G4 strain. In some embodiments, the pharmaceutical probioticcomposition comprises an additional strain of bacteria, wherein theadditional strain comprises Propionibacterium avidum orPropionibacterium granulosum. In some embodiments, the additional straincomprises Propionibacterium acnes subsp. defendens.

In some aspects, disclosed herein are pharmaceutical probioticcompositions that comprise: (a) a first therapeutically effective amountof a health-associated Propionibacterium acnes microbe, wherein thefirst health-associated Propionibacterium acnes microbe is characterizedby at least one of the following: comprises at least one gene encodingat least one of a deoxyribose operon repressor and a type II lipase, andless than about 10% pIMPLE plasmid; comprises at least one gene encodingan ATP binding cassette transporter; or lacks at least one gene encodinga DNA binding response regulator or a phosphoglycerate kinase; (b) asecond therapeutically effective amount of a second health-associatedmicrobe, wherein the second health-associated microbe has beenengineered or selected to comprise at least one gene encoding at leastone of a deoxyribose operon repressor and a type II lipase, and lessthan about 10% pIMPLE plasmid; and (c) a pharmaceutically acceptableexcipient or biological stabilizer. In some embodiments, the secondhealth-associated microbe is a strain of bacteria comprising P. acnes,P. granulosum, or P. avidum. In some embodiments, the secondhealth-associated microbe is a strain of bacteria comprisingPropionibacterium acnes subsp. defendens.

In some aspects, disclosed herein are pharmaceutical compositions thatcomprise: (a) a pharmaceutically acceptable excipient or biologicalstabilizer; and (b) a therapeutically effective amount of ahealth-associated Propionibacterium acnes microbe, wherein thehealth-associated Propionibacterium acnes microbe does not express a DNAbinding response regulator, a phosphoglycerate kinase, or a combinationthereof. In some aspects, disclosed herein are pharmaceuticalcompositions that comprise: (a) a pharmaceutically acceptable excipientor biological stabilizer; and (b) a therapeutically effective amount ofa health-associated Propionibacterium acnes microbe, wherein thehealth-associated Propionibacterium acnes microbe expresses anATP-binding cassette transporter. In some aspects, disclosed herein arepharmaceutical compositions that comprise: (a) a pharmaceuticallyacceptable excipient or biological stabilizer; and (b) a therapeuticallyeffective amount of a health-associated Propionibacterium acnes microbe,wherein the health-associated Propionibacterium acnes microbe: does notexpress a DNA binding response regulator, a phosphoglycerate kinase, ora combination thereof; and expresses an ATP-binding cassettetransporter. In some embodiments, the DNA binding response regulator isencoded by a sequence of SEQ ID NO: 7. In some embodiments, the DNAbinding response regulator is encoded by a sequence that is at least 50%homologous to a sequence of SEQ ID NO: 7. In some embodiments, thephosphoglycerate kinase is encoded by a sequence of SEQ ID NO: 9. Insome embodiments, the phosphoglycerate kinase is encoded by a sequencethat is at least 50% homologous to a sequence of SEQ ID NO: 9. In someembodiments, the ATP-binding cassette transporter is encoded by asequence of SEQ ID NO: 6. In some embodiments, the ATP-binding cassettetransporter is encoded by a sequence that is at least 50% homologous toa sequence of SEQ ID NO: 6. In some embodiments, the pharmaceuticalcomposition comprises at least two strains of bacteria. In someembodiments, the pharmaceutical composition comprises a strain ofPropionibacterium acnes having a ribotype of RT1, RT2, RT3, RT4 or RT5.In some embodiments, the pharmaceutical composition comprises a strainof Propionibacterium acnes having a ribotype of RT1 or RT2. In someembodiments, the health-associated Propionibacterium acnes microbe doesnot comprise an RT6 ribotype. In some embodiments, the pharmaceuticalcomposition is formulated for topical administration. In someembodiments, the pharmaceutical composition is in the form of a gel,ointment, lotion, emulsion, paste, cream, foam, mousse, liquid, spray,suspension, dispersion and aerosol. In some embodiments, thepharmaceutical composition comprises a liposome or nanoparticle. In someembodiments, the health-associated Propionibacterium acnes microbecomprises a deoxyribose operon repressor and a type II lipase. In someembodiments, a Cas5 protein is absent from the health-associatedPropionibacterium acnes microbe. In some embodiments, thehealth-associated Propionibacterium acnes microbe comprises less thanabout 1% pIMPLE plasmid. In some embodiments, the health-associatedPropionibacterium acnes microbe comprises less than about 0.3% pIMPLEplasmid. In some embodiments, the health-associated Propionibacteriumacnes microbe comprises a mixture of two or more different ribotypes ofPropionibacterium acnes. In some embodiments, the pharmaceuticallyacceptable excipient or biological stabilizer increases the viability ofthe health-associated Propionibacterium acnes microbe at a temperaturefrom about −10° C. to about 30° C. In some embodiments, thepharmaceutical composition comprises an additional strain of bacteria.In some embodiments, the pharmaceutical composition comprises anadditional strain of bacteria, wherein the additional strain comprisesPropionibacterium avidum and Propionibacterium granulosum. In someembodiments, the additional strain comprises Propionibacterium acnessubsp. defendens. In some embodiments, the health-associatedPropionibacterium acnes microbe is selected, transformed or engineeredto: (a) comprise at least one gene encoding at least one of adeoxyribose operon repressor and a type II lipase, and less than about10% pIMPLE plasmid; (b) comprise at least one gene encoding an ATPbinding cassette transporter; or (c) lack at least one gene encoding aDNA binding response regulator or a phosphoglycerate kinase.

In some aspects, methods of treating a skin disorder or condition areprovided comprising applying a therapeutically effective amount of apharmaceutical composition disclosed herein. In some embodiments, theskin disorder or condition comprises acne, eczema, seborrheicdermatitis, psoriasis, or rosacea, or a combination thereof.

In some aspects, disclosed herein are pharmaceutical probioticcompositions comprising: (a) a therapeutically effective amount of ahealth-associated Propionibacterium acnes microbe, wherein thehealth-associated Propionibacterium acnes microbe has been engineered orselected to comprise at least one gene encoding at least one of adeoxyribose operon repressor and a type II lipase, and less than about10% pIMPLE plasmid; and (b) a pharmaceutically acceptable excipient orbiological stabilizer. In some embodiments, the health-associatedPropionibacterium acnes microbe has been engineered or selected tocomprise a deoxyribose operon repressor and a type II lipase. In someembodiments, a Cas 5 protein is absent from the health-associatedPropionibacterium acnes microbe. In some embodiments, thehealth-associated Propionibacterium acnes microbe comprises an RT1 orRT2 ribotype. In some embodiments, the health-associatedPropionibacterium acnes microbe does not comprise an RT6 ribotype. Insome embodiments, the health-associated Propionibacterium acnes microbecomprises less than about 1% pIMPLE plasmid. In some embodiments, thehealth-associated Propionibacterium acnes microbe comprises less thanabout 0.3% pIMPLE plasmid. In some embodiments, the health-associatedPropionibacterium acnes microbe comprises a mixture of two or moredifferent ribotypes of Propionibacterium acnes. In some embodiments, thepharmaceutically acceptable excipient or biological stabilizer increasesthe viability of the health-associated Propionibacterium acnes microbeat a temperature from about −10° C. to about 30° C. In some embodiments,the health-associated Propionibacterium acnes microbe comprises anHP3A11 strain, an HP3B4 strain, an HP4G1, or an HP5G4 strain. In someembodiments, the pharmaceutical probiotic composition comprises anadditional strain of bacteria, wherein the additional strain comprisesPropionibacterium avidum or Propionibacterium granulosum. In someembodiments, the additional strain comprises Propionibacterium acnessubsp. defendens. In some embodiments, the health-associatedPropionibacterium acnes microbe expresses an ATP binding cassettetransporter. In some embodiments, the health-associatedPropionibacterium acnes microbe does not express a DNA binding responseregulator or a phosphoglycerate kinase.

In some aspects, disclosed herein are methods of treating a skindisorder or condition comprising applying a therapeutically effectiveamount of a pharmaceutical probiotic composition comprising: (a) atherapeutically effective amount of a health-associatedPropionibacterium acnes microbe, wherein the health-associatedPropionibacterium acnes microbe has been engineered or selected tocomprise at least one gene encoding at least one of a deoxyribose operonrepressor and a type II lipase, and less than about 10% pIMPLE plasmid;and (b) a pharmaceutically acceptable excipient or biologicalstabilizer. In some embodiments, the skin disorder or conditioncomprises acne, eczema, seborrheic dermatitis, psoriasis, or rosacea. Insome embodiments, the health-associated Propionibacterium acnes microbehas been engineered or selected to at least one gene encoding thedeoxyribose operon repressor and the type II lipase. In someembodiments, the Cas5 protein is absent from the health-associatedPropionibacterium acnes microbe. In some embodiments, thehealth-associated Propionibacterium acnes microbe comprises an RT1 orRT2 ribotype. In some embodiments, the health-associatedPropionibacterium acnes microbe does not comprise an RT6 ribotype. Insome embodiments, the health-associated Propionibacterium acnes microbecomprises less than about 1% pIMPLE plasmid. In some embodiments, thehealth-associated Propionibacterium acnes microbe comprises less thanabout 0.3% pIMPLE plasmid. In some embodiments, the health-associatedPropionibacterium acnes microbe comprises a mixture of two or moredifferent ribotypes. In some embodiments, the pharmaceuticallyacceptable excipient or biological stabilizer increases the viability ofthe health-associated Propionibacterium acnes microbe at a temperaturefrom about −10° C. to about 30° C. In some embodiments, thehealth-associated Propionibacterium acnes microbe comprises at least oneof an HP3A11 strain, an HP3B4 strain, or HP4G1 strain, or an HP5G4strain. In some embodiments, the pharmaceutical probiotic compositioncomprises an additional strain of bacteria, wherein the additionalstrain comprises Propionibacterium avidum or Propionibacteriumgranulosum. In some embodiments, the additional strain comprisesPropionibacterium acnes subsp. defendens.

In some aspects, disclosed herein are pharmaceutical probioticcompositions comprising: (a) a first therapeutically effective amount ofa first health-associated Propionibacterium acnes microbe, wherein thefirst health-associated Propionibacterium acnes microbe has beenengineered or selected to at least one gene encoding at least one of adeoxyribose operon repressor and a type II lipase, and less than about10% pIMPLE plasmid; (b) a second therapeutically effective amount of asecond health-associated Propionibacterium acnes microbe, wherein thesecond health-associated Propionibacterium acnes microbe has beenengineered or selected to comprise at least one gene encoding at leastone of a deoxyribose operon repressor and a type II lipase, and lessthan about 10% pIMPLE plasmid; and (c) a pharmaceutically acceptableexcipient or biological stabilizer. In some embodiments, the first orthe second health-associated Propionibacterium acnes microbe has beenengineered or selected to comprise: (i) at least one gene encoding thedeoxyribose operon repressor and the type II lipase, (ii) at least onegene encoding the deoxyribose operon repressor and less than about 10%pIMPLE plasmid, or (iii) at least one gene encoding the type II lipaseand less than about 10% pIMPLE plasmid. In some embodiments, the firstand the second health-associated Propionibacterium acnes microbe hasbeen engineered or selected to comprise: (i) at least one gene encodingthe deoxyribose operon repressor and the type II lipase, (ii) at leastone gene encoding the deoxyribose operon repressor and less than about10% pIMPLE plasmid, or (iii) at least one gene encoding the type IIlipase and less than about 10% pIMPLE plasmid. In some embodiments, thefirst or the second health-associated Propionibacterium acnes microbehas been engineered or selected to comprise at least one gene encodingthe deoxyribose operon repressor, the type II lipase, and less thanabout 10% pIMPLE plasmid. In some embodiments, the first and the secondhealth-associated Propionibacterium acnes microbe has been engineered orselected to comprise at least one gene encoding the deoxyribose operonrepressor, the type II lipase, and less than about 10% pIMPLE plasmid.In some embodiments, the first and the second health-associatedPropionibacterium acnes microbes are different strains. In someembodiments, the first or the second health-associated Propionibacteriumacnes microbe comprises an RT1 or RT2 ribotype. In some embodiments, thefirst health-associated Propionibacterium acnes microbe comprises an RT1ribotype and the second health-associated Propionibacterium acnesmicrobe comprises an RT2 ribotype. In some embodiments, neither thefirst nor the second health-associated Propionibacterium acnes microbecomprises an RT6 ribotype. In some embodiments, the pharmaceuticallyacceptable excipient or biological stabilizer increases the viability ofthe health-associated. Propionibacterium acnes microbe at a temperaturefrom about −10° C. to about −30° C. In some embodiments, thehealth-associated Propionibacterium acnes microbe comprises at least oneof an HP3A11 strain, an HP3B4 strain, or HP4G1 strain, or an HP5G4strain. In some embodiments, the first or second health-associatedPropionibacterium acnes microbe expresses an ATP binding cassettetransporter. In some embodiments, the first or second health-associatedPropionibacterium acnes microbe does not express a DNA binding responseregulator or a phosphoglycerate kinase. In some aspects, thepharmaceutical probiotic compositions disclosed herein are for use inthe treatment of a skin disorder or condition.

In some aspects, disclosed herein are methods of producing a desiredpreparation of a Propionibacterium acnes bacteria, said methodcomprising: (a) adding a sample of the Propionibacterium acnes bacteriato a glycerol solution to produce a Propionibacterium acnes glycerolstock, and (b) storing the Propionibacterium acnes glycerol stock at atemperature of about 4° C. or less, wherein more than about 50% of theP. acnes bacteria is viable when the Propionibacterium acnes bacteria inthe glycerol solution is brought to ambient temperature. In someembodiments, the glycerol solution is between about 25% and about 75%glycerol. In some embodiments, the glycerol solution is about 50%glycerol. In some embodiments, the temperature is between about 4° C.and about −80° C. In some embodiments, the temperature is about −20° C.In some embodiments, at least about 70% to at least about 90% of thesample is viable after the Propionibacterium acnes glycerol stock isbrought to ambient temperature. In some embodiments, at least about 90%of the sample is viable after the Propionibacterium acnes glycerol stockis brought to ambient temperature. In some embodiments, the ambienttemperature is between about 20° C. and about 30° C. In someembodiments, the ambient temperature is about 25° C. In someembodiments, the Propionibacterium acnes glycerol stock is brought toambient temperature before about 90 days of initiating storing. In someembodiments, more than 50% of the sample is viable after about 20 daysof storing. In some embodiments, more than about 50% of the sample isviable after about 90 days of storing. In some embodiments, more thanabout 50% of the sample is viable at least up to about 90 days ofstoring. In some embodiments, the Propionibacterium acnes bacteriacomprises an HP3A11 strain, an HP3B4 strain, or HP4G1 strain, or anHP5G4 strain.

In some aspects, disclosed herein are methods of producing a desiredpreparation of a preserved Propionibacterium acnes sample, wherein atleast about 90% of said preserved Propionibacterium acnes sample isviable after sixty days of storage, said method comprising: (a) adding asample of Propionibacterium acnes bacteria to a solution of betweenabout 25% and about 50% glycerol in phosphate buffered saline solutionto produce a Propionibacterium acnes glycerol stock; and (b) cooling thePropionibacterium acnes glycerol stock at a temperature from about −20°C. to about 4° C., thereby forming said desired preparation wherein atleast about 90% of said sample of Propionibacterium acnes bacteria isviable after sixty days of storage. In some aspects, disclosed hereinare methods of producing a desired preparation of a preservedPropionibacterium acnes sample, wherein at least about 90% of saidpreserved Propionibacterium acnes sample is viable after ninety days ofstorage, said method comprising: adding a sample of Propionibacteriumacnes bacteria to a solution of about 50% glycerol to produce aPropionibacterium acnes glycerol stock; and freezing thePropionibacterium acnes glycerol stock at −20° C., thereby forming saiddesired preparation wherein at least about 90% of said sample ofPropionibacterium acnes bacteria is viable after a thawing of thePropionibacterium acnes glycerol stock. In some embodiments, the methodscomprise thawing the Propionibacterium acnes glycerol stock at roomtemperature. In some embodiments, the solution is about 25-50% glycerolv/v in water. In some embodiments, the solution is about 25-50% glycerolv/v in a buffered solution. In some embodiments, the buffered solutionis a phosphate buffered saline. In some embodiments, the bufferedsolution is an acetate buffered solution. In some embodiments, thesolution comprises potassium. In some embodiments, the solutioncomprises potassium at a concentration of about 150 mM to about 200 mM.In some embodiments, the solution comprises calcium. In someembodiments, the solution comprises calcium at a concentration of about0.05 mM to about 0.1 mM. In some embodiments, the solution comprises aprebiotic stabilizing agent. In some embodiments, the prebioticstabilizing agent is inulin. In some embodiments, the inulin is presentin the solution at a concentration of about 0.05% v/v to about 0.2% v/v.In some embodiments, the solution comprises an anti-acne agent. In someembodiments, the anti-acne agent comprises a retinoid, a vitamin, anantioxidant, a peroxide, an acid, an oil, an alcohol, an extract, or ananalog thereof. In some embodiments, the retinoid comprises tretinoin,tazarotene, adapalene, or retinol. In some embodiments, the vitamin oranalog thereof comprises Vitamin D, Vitamin C, Vitamin E, orcalciptotriene. In some embodiments, the antioxidant comprises Vitamin Cor Vitamin E. In some embodiments, the peroxide is benzoyl peroxide. Insome embodiments, the acid comprises salicylic acid, azaelic acid,trichloracetic acid, or glycolic acid. In some embodiments, the alcoholcomprises retinol or resveratrol. In some embodiments, the oil is teatree oil. In some embodiments, the extract is a green tea extract. Insome embodiments, the solution is incorporated in a biologic stabilityplatform to eliminate cold chain storage. In some embodiments, thebiologic storage platform comprises foam drying or foam formation of thesolution or glycerol stock solution. In some embodiments, the solutioncomprises at least one of a glyconanoparticle, a liposome, ananoparticle, trehalose, sucrose, stachyose, hydroxyethyl starch, or acombination of glycine and mannitol. In some embodiments, the sample ofPropionibacterium acnes bacteria comprises Propionibacterium acnesbacteria of ribotype RT1. In some embodiments, the sample ofPropionibacterium acnes bacteria comprises Propionibacterium acnesbacteria of ribotype RT2. In some embodiments, the sample ofPropionibacterium acnes bacteria comprises Propionibacterium acnesbacteria of ribotype RT1 and RT2. In some embodiments, thePropionibacterium acnes bacteria is characterized by at least one of thefollowing: comprises a deoR protein; comprises a type II lipase;comprises less than 10% pIMPLE plasmid; does not comprise a Cas5protein; comprises an ATP binding cassette transporter protein; does notcomprise a DNA binding response regulator; and does not comprise aphosphoglycerate kinase. In some embodiments, the sample ofPropionibacterium acnes bacteria comprises Propionibacterium acnes anHP3A11 strain, an HP3B4 strain, or HP4G1 strain, or an HP5G4 strain.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 illustrates exemplary production and packaging of compositions ofhealth-associated microbes disclosed herein. Dashed lines indicateoptional steps.

FIG. 2 shows the percentage of reads from a sample of a healthyvolunteer (free of acne) that map to P. acnes to ribotype RT1, which areboth deoR+ and type II lipase positive, versus the percentage of readsfrom the samples that map to P. acnes RT2.

FIG. 3 shows results of an assay for P. acnes viability under differentpreservation conditions.

FIG. 4 shows a portion of a 23S, ribosomal RNA sequence from bacteriacommonly found on the human face that enables characterization of asubject's skin microbiome. Numbers listed to the left of sequencescorrespond to bacterial strains as follows: (1) P.acnes_KPA171202_RT1_2; (2) P. acnes_KPA171202_RT1_3; (3) P. acnes ATCC11828_RT2_1; (4) P. acnes ATCC 11828_RT2_2; (5) P. avidum 44067; (6) P.acidipropionici ATCC 4875; (7) S. aureus 04-02981; (8) S. aureusBmb9393; (9) S. aureus FDA209P; (10) S. epidermidis ATCC 12228; and (11)S. epidermidis PM221. Sequences 1-5 correspond to SEQ ID NOs: 33 to 37.Sequence 6 corresponds to SEQ ID NO: 38. Sequences 7-11 correspond toSEQ ID NOs: 39-43.

FIG. 5 shows a standard curve generated with serial dilutions of acombination of health-associated P. acnes and S. epidermidis that can beused to quantitate a percentage of health-associated P. acnes in acollected sample.

FIG. 6 shows qPCR of successful CRISPR editing in P. acnes.

FIG. 7 shows mutations in a gene encoding a P. acnes type I lipase thatresult in a gene encoding a P. acnes type II lipase. Type I lipaseIntergenic Region corresponds to SEQ ID NO.: 44. Type I lipase SecondLipase (region) (HMPREF0675_4856) corresponds to SEQ ID NOS: 45, 46 and47, respectively, in order of appearance. Type II lipase Second Lipase(region) (HMPREF0675_4856) corresponds to SEQ ID NOS: 50, 55 and 56,respectively, in order of appearance. Type I lipase Intergenic Regioncorresponds to SEQ ID NO.: 44. Type II lipase Intergenic Regioncorresponds to SEQ ID NO.: 49. SEQ ID NO: 57 is disclosed as thesequence extending from the Type I lipase Intergenic Region through thenext 12 residues in the Type I lipase Second Lipase (region). SEQ ID NO:58 is disclosed as the sequence extending from the Type II lipaseIntergenic Region through the next 12 residues in the Type II lipaseSecond Lipase (region).

FIG. 8 shows exemplary packaging for compositions disclosed herein.

FIG. 9 shows bacteria viability of composition disclosed herein afterbeing packaged under several conditions.

DETAILED DESCRIPTION OF THE INVENTION

In the following description, certain specific details are set forth inorder to provide a thorough understanding of various embodiments.However, one skilled in the art will understand that the embodimentsprovided may be practiced without these details. Unless the contextrequires otherwise, throughout the specification and claims whichfollow, the word “comprise” and variations thereof, such as, “comprises”and “comprising” are to be construed in an open, inclusive sense, thatis, as “including, but not limited to.” As used in this specificationand the appended claims, the singular forms “a,” “an,” and “the” includeplural referents unless the content clearly dictates otherwise. Itshould also be noted that the term “or” is generally employed in itssense including “and/or” unless the content clearly dictates otherwise.Further, headings provided herein are for convenience only and do notinterpret the scope or meaning of the claimed embodiments.

As used herein the term “about” refers to an amount that is near thestated amount by about 10%, 5%, or 1%.

As used herein “consisting essentially of” when used to definecompositions and methods, shall mean excluding other elements of anyessential significance to the combination for the stated purpose. Thus,a composition consisting essentially of the elements as defined hereinwould not exclude other materials or steps that do not materially affectthe basic and novel characteristic(s) of the claimed disclosure, such ascompositions for treating skin disorders like acne, eczema, psoriasis,and rosacea.

As used herein “health-associated” means a microbe that is moreprevalent in healthy or disease free individuals than in individualsdiagnosed with a given disorder. In certain embodiments, the disease maybe acne, eczema, seborrheic dermatitis, psoriasis, rosacea, or anycombination thereof. A health-associated microbe can be determinedstatistically. For example, by comparing the microbiome or theprevalence of certain microbial species or strains on the skin, in theoral cavity, or in the digestive system of a healthy non-diseaseafflicted individual as compared to an individual with a given disease.Genera, species, or strains that are more prevalent in/on healthyindividuals are health-associated. A health-associated strain can alsobe a strain that has been genetically modified or selected to expresslow levels of virulence factors that are associated with a given skindisease. A health-associated strain can also be a strain that has beengenetically modified or selected to express high levels of beneficialgenes, RNAs, or proteins that are associated with protection from agiven skin disease. A health-associated strain can also be a strain thathas been genetically modified or selected to express, not express, orexpress desirable levels of markers, as described herein.

As used herein a “probiotic’ is a microbe that provides health benefitswhen consumed or applied. In some instances, probiotics disclosed hereinare microbes that inhibit the activity or growth of a disease causingbacteria associated with acne, eczema, seborrheic dermatitis, psoriasis,or rosacea.

As used herein, the terms “homologous,” “homology,” or “percenthomology” when used herein to describe to an amino acid sequence or anucleic acid sequence, relative to a reference sequence, can bedetermined using the formula described by Karlin and Altschul (Proc.Natl. Acad. Sci. USA 87: 2264-2268, 1990, modified as in Proc. Natl.Acad. Sci. USA 90:5873-5877, 1993). Such a formula is incorporated intothe basic local alignment search tool (BLAST) programs of Altschul etal. (J. Mol. Biol. 215: 403-410, 1990). Percent homology of sequencescan be determined using the most recent version of BLAST, as of thefiling date of this application.

Strains of Propionibacterium acnes, HP3A11, HP4G1 and HP5G4, describedherein, were deposited in the American Tissue Culture Collection (10801University Boulevard Manassas, Va. 20110-2209 USA) on Apr. 6, 2017 inaccordance with and under the provisions of the Budapest Treaty for theInternational Recognition of the Deposit of Microorganisms for thePurpose of Patent Procedure. The strains were tested by the ATCC anddetermined to be viable. The ATCC has assigned ATCC deposit accessionnumbers: PTA-124010 to strain HP3A11; PTA-124011 to strain HP4G1; andPTA 124012 to HP5G4.

Provided throughout this application are compositions and methods forthe treatment of skin disorders. It is should be understood thatcompositions disclosed herein may be used according to methods describedherein. Conversely, methods disclosed herein may appropriately employcompositions disclosed herein.

Compositions for Treatments of Skin Disorders

In some aspects, the disclosure provides compositions comprising astrain of bacteria. The strain of bacteria is generally a strain thatpromotes, restores or improves skin health. In some embodiments,compositions disclosed herein comprise at least one health-associatedstrain of bacteria. In some embodiments, the at least onehealth-associated strain of bacteria is a strain of Propionibacteriumbacteria. In some embodiments, the at least one health-associated strainof bacteria is a strain of Staphylococcus bacteria. In some embodiments,the at least one health-associated strain of bacteria is a strain ofLactobacillus bacteria. In some embodiments, the composition isformulated for application to the skin of a subject.

In some embodiments, compositions disclosed herein comprise a fungus.The fungus is generally a fungus that promotes, restores or improvesskin health. In some embodiments, compositions disclosed herein compriseat least one health-associated fungus. In some embodiments, the fungusis Malassezia.

In some embodiments, compositions disclosed herein comprise abacteriophage, also referred to herein as a phage for simplicity. Insome embodiments, the bacteriophage is a Propionibacterium phage. Insome embodiments, the bacteriophage is a health-associatedPropionibacterium phage. In some embodiments, the health-associatedPropionibacterium phage is a phage found on skin of a subject that isfree of a skin disorder. In some embodiments, the health-associatedPropionibacterium phage is a phage found on skin of a subject that isfree of acne. In some embodiments, the health-associatedPropionibacterium phage is a phage found on skin of a subject that isfree of eczema. In some embodiments, the health-associatedPropionibacterium phage is a phage found on skin of a subject that isfree of psoriasis. In some embodiments, the health-associatedPropionibacterium phage is a phage found on skin of a subject that isfree of seborrheic dermatitis. In some embodiments, thehealth-associated Propionibacterium phage is a phage found on skin of asubject that is free of rosacea. In some embodiments, thehealth-associated Propionibacterium phage is a phage that is moreabundant or prevalent on skin free of a skin disorder than skin with askin disorder. In some embodiments, the bacteriophage is aPropionibacterium acnes phage. In some embodiments, thePropionibacterium acnes phage targets a select strain of P. acnes. Insome embodiments, the Propionibacterium acnes phage targets a pathogenicstrain of P. acnes. Non-limiting examples of Propionibacterium acnesphages are described in Farrar et al. (2007) J. Bacteriol., vol. 189,pp. 4161-4167, and Liu et al. (2015) ISME J, vol. 9, pp. 2078-2093.

In some embodiments, the at least one health-associated strain ofbacteria is a strain of Propionibacterium acnes (referred to herein asP. acnes). In some embodiments, the at least one health-associatedstrain of bacteria is not a strain of P. acnes subsp. acnes. In someembodiments, the at least one health-associated strain of bacteria is astrain of Propionibacterium avidum (referred to herein as P. avidum). Insome embodiments, the at least one health-associated strain of bacteriais a strain of Propionibacterium granulosum (referred to herein as P.granulosum). In some embodiments, the at least one health-associatedstrain of bacteria is a strain of Propionibacterium acnes subsp.defendens (referred to herein as P. acnes subsp. defendens), In someembodiments, the at least one health-associated strain of bacteria is astrain of Staphylococcus aureus. In some embodiments, the at least onehealth-associated strain of bacteria is a strain of Staphylococcusepidermidis. In some embodiments, the at least one health-associatedstrain of bacteria is a strain of Staphylococcus hominis. In someembodiments, the at least one health-associated strain of bacteria is astrain of Lactobacillus reuteri. In some embodiments, the strain ofbacteria is associated with healthy skin or normal skin, and is referredto as a probiotic (or live biologic therapeutic). In some embodiments,the probiotic is associated with skin that is free of acne. In someembodiments, the probiotic is associated with skin that is essentiallyfree of acne.

Provided herein are compositions that comprise at least one probioticdisclosed herein. In some embodiments, a probiotic disclosed herein isselected or assessed for a composition for treatment by assessing anamount of inflammation that is caused by the probiotic to the skin of asubject. In some embodiments, the probiotic produces or induces a lowamount of pro-inflammatory mediators when applied to a subject's skin.In some embodiments, the probiotic produces or induces a low amount ofpro-inflammatory mediators when applied to a subject's skin. In someembodiments, the probiotic does not produce or induce pro-inflammatorymediators when applied to a subject's skin. In some embodiments, theprobiotic does not produce or induce pro-inflammatory mediators whenapplied to a subject's skin. In some embodiments, the probiotic does notproduce or induce an amount of pro-inflammatory mediators sufficient tocause acne of a subject when applied to a subject's skin. In someembodiments, the probiotic does not produce or induce an amount ofpro-inflammatory mediators sufficient to worsen acne of a subject whenapplied to a subject's skin. The probiotic may not induce humaninflammatory associated mRNAs such as interleukins, chemokine orcytokines when applied to a subject's skin. The probiotic may induceonly low amounts of human inflammatory associated mRNAs such asinterleukins, chemokine or cytokines, when applied to a subject's skin.

In some embodiments, a probiotic disclosed herein is selected orassessed by incubating a sample of keratinocytes with the probiotic. Insome embodiments, the probiotic produces or induces a low amount ofpro-inflammatory mediators when co-incubated with a subject'skeratinocytes. In some embodiments, the probiotic produces or induces alow amount of pro-inflammatory mediators when co-incubated with skinkeratinocytes that are pooled from multiple subjects. In someembodiments, the probiotic does not produce or induce pro-inflammatorymediators when co-incubated with a subject's keratinocytes. In someembodiments, the probiotic does not produce or induce pro-inflammatorymediators when co-incubated with skin keratinocytes pooled from multiplesubjects (e.g., “pooled skin keratinocytes”). In some embodiments, theprobiotic comprises does not produce or induce an amount ofpro-inflammatory mediators sufficient to cause acne of a subject whenco-incubated with the subject's keratinocytes or pooled skinkeratinocytes. In some embodiments, the probiotic does not produce orinduce an amount of pro-inflammatory mediators sufficient to worsen acneof a subject when co-incubated with a subject's keratinocytes or pooledskin keratinocytes. The probiotic may not induce human inflammatoryassociated mRNAs such as interleukins, chemokine or cytokines whenincubated with a subjects own keratinocytes or pooled keratinocytes froma plurality of healthy volunteers. The probiotic may induce only lowamounts of human inflammatory associated mRNAs such as interleukins,chemokine or cytokines, when incubated with a subjects own keratinocytesor pooled keratinocytes from a plurality of healthy volunteers. Theprobiotic may induce only low amounts of human inflammatory associatedmRNAs or proteins such as interleukins, chemokine or cytokines, whenincubated with primary human monocytes. In a certain embodiment, theinflammatory interleukin, chemokine or cytokine comprises IL-2, IL-12,or MCP-1. An exemplar assay for induction of IL-12 in monocytes by abacterium can be found in U.S. Pat. No. 9,549,905.

Compositions disclosed herein may comprise a strain the produces lowlevels of at least one porphyrin. In some embodiments, the strainproduces undetectable levels of the at least one porphyrin. Non-limitingexamples of porphyrins include coproporphyrin III and protoporphyrin IX.In some embodiments, a low level of the at least one porphyrin is lessthan about 1 micromolar. In some embodiments, a low level of the atleast one porphyrin is less than about 750 nanomolar. In someembodiments, a low level of the at least one porphyrin is less thanabout 500 nanomolar. In some embodiments, a low level of the at leastone porphyrin is less than about 250 nanomolar. In some embodiments, alow level of the at least one porphyrin is less than about 200nanomolar. In some embodiments, a low level of the at least oneporphyrin is less than about 150 nanomolar. In some embodiments, a lowlevel of the at least one porphyrin is less than about 100 nanomolar. Insome embodiments, a low level of the at least one porphyrin is less thanabout 50 nanomolar. In some embodiments, a low level of the at least oneporphyrin is less than about 10 nanomolar. In some embodiments, a lowlevel of the at least one porphyrin is less than about 1 nanomolar. Insome embodiments, the low level is a level measured in vitro. In someembodiments, the low level is a level measured in situ, due tofluorescent properties of porphyrins. In some embodiments, a strain isgenetically modified to delete or mutate a nucleic acid encoding anenzyme in a porphyrin production pathway to effectively create or selectfor strains with low porphyrin production. In some embodiments, thestrain has low lipase activity as compared to a pathogenic strain ofbacteria. In some embodiments, the strain has low immunogenicity ascompared to a pathogenic strain of bacteria.

Disclosed herein are pharmaceutical compositions that comprise: (a) afirst therapeutically effective amount of a first health-associatedPropionibacterium microbe, wherein the first health-associatedPropionibacterium microbe produces less than about one micromolarporphyrin; (b) a second therapeutically effective amount of a secondhealth-associated microbe; and (c) a pharmaceutically acceptableexcipient or biological stabilizer. Further disclosed herein arepharmaceutical compositions that consist essentially of: (a) a firsttherapeutically effective amount of a first health-associatedPropionibacterium microbe, wherein the first health-associatedPropionibacterium microbe produces less than about one micromolarporphyrin; (b) a second therapeutically effective amount of a secondhealth-associated microbe; (c) a pharmaceutically acceptable excipientor biological stabilizer; and (d) optionally, an additional activeingredient disclosed herein. In some embodiments, the secondhealth-associated microbe comprises a strain of Propionibacterium. Insome embodiments, the concentration of porphyrin is a concentrationmeasured in vitro. In some embodiments, the concentration of porphyrinis a concentration measured in situ. For example, porphyrinconcentration can be measured directly on skin of a subject using lightof a wavelength around 400 nm, a camera that detects fluorescence, anddigital imaging software that quantifies fluorescence. In someembodiments, light of a wavelength between 300 and 900 nm is used.

In some embodiments, the first health-associated microbe produces lessthan about one micromolar porphyrin

In some embodiments, the second health-associated microbe produces lessthan about one micromolar porphyrin.

In some embodiments, the first health-associated Propionibacteriummicrobe and the second health-associated Propionibacterium microbecollectively produce less than about one micromolar porphyrin. In someembodiments, the first health-associated Propionibacterium microbe andthe second health-associated Propionibacterium microbe collectivelyproduce less than about 800 nanomolar porphyrin. In some embodiments,the first health-associated Propionibacterium microbe and the secondhealth-associated Propionibacterium microbe collectively produce lessthan about 500 nanomolar porphyrin. In some embodiments, the firsthealth-associated Propionibacterium microbe and the secondhealth-associated Propionibacterium microbe collectively produce lessthan about 200 nanomolar porphyrin. In some embodiments, the firsthealth-associated Propionibacterium microbe and the secondhealth-associated Propionibacterium microbe collectively produce lessthan about 100 nM porphyrin. In some embodiments, the firsthealth-associated Propionibacterium microbe and the secondhealth-associated Propionibacterium microbe collectively produce lessthan about 10 nM porphyrin.

In some embodiments, the first health-associated Propionibacteriummicrobe comprises a strain of Propionibacterium acnes, Propionibacteriumgranulosum, Propionibacterium avidum, or Propionibacterium acnes subsp.defendens. In some embodiments, the second health-associatedPropionibacterium microbe comprises a strain of Propionibacterium acnes,Propionibacterium granulosum, Propionibacterium avidum, orPropionibacterium acnes subsp. defendens. In some embodiments, the firsthealth-associated Propionibacterium microbe comprises a strain ofPropionibacterium acnes. In some embodiments, the secondhealth-associated Propionibacterium microbe comprises a strain ofPropionibacterium acnes. In some embodiments, the firsthealth-associated Propionibacterium microbe comprises aPropionibacterium acnes of a ribotype RT1 or RT2. In some embodiments,the second health-associated Propionibacterium microbe comprises aPropionibacterium acnes of a ribotype RT1 or RT2. In some embodiments,the first health-associated Propionibacterium microbe: (a) comprises atleast one gene encoding an ATP binding cassette transporter; (b)comprises at least one gene encoding at least one of a deoxyriboseoperon repressor and a type II lipase, and less than about 10% pIMPLEplasmid; or (c) lacks at least one gene encoding a DNA binding responseregulator or a phosphoglycerate kinase. In some embodiments, the secondhealth-associated Propionibacterium microbe: (a) comprises at least onegene encoding an ATP binding cassette transporter; (b) comprises atleast one gene encoding at least one of a deoxyribose operon repressorand a type II lipase, and less than about 10% pIMPLE plasmid; or (c)lacks at least one gene encoding a DNA binding response regulator or aphosphoglycerate kinase.

Probiotic strains disclosed herein may be defined by 16S, 18S, or 23Sribosomal DNA sequences, metagenomic DNA, the presence of specifichealth-associated markers, the absence of disease associated markers, ora combination thereof. Probiotic strains disclosed herein may beenriched or isolated to obtain a purified strain.

Provided herein are compositions comprising not more than one isolatedstrain of bacteria disclosed herein. Provided herein are compositionscomprising not more than two isolated strains of bacteria disclosedherein. Provided herein are compositions comprising not more than threeisolated strains of bacteria disclosed herein. Provided herein arecompositions comprising not more than four isolated strains of bacteriadisclosed herein. Provided herein are compositions comprising not morethan five isolated strains of bacteria disclosed herein. Provided hereinare compositions comprising not more than six isolated strains ofbacteria disclosed herein. Provided herein are compositions comprisingnot more than seven isolated strains of bacteria disclosed herein.Provided herein are compositions comprising not more than eight isolatedstrains of bacteria disclosed herein. Provided herein are compositionscomprising not more than nine isolated strains of bacteria disclosedherein. Provided herein are compositions comprising not more than tenisolated strains of bacteria disclosed herein.

Probiotics disclosed herein may comprise at least one strain of bacteriathat inhibits the activity of a pathogenic strain of P. acnes. In someembodiments, the probiotic is bacteriostatic or bactericidal for apathogenic strain of P. acnes. In some embodiments, the probioticreduces growth, re-growth or metabolism of the pathogenic strain of P.acnes. In certain embodiments, the probiotic reduces growth (orre-growth) of the pathogenic P. acnes by at least about 20% as comparedto placebo/no probiotic. In certain embodiments, the probiotic reducesgrowth (or re-growth) of the pathogenic P. acnes by at least about 30%.In certain embodiments, the probiotic reduces growth (or re-growth) ofthe pathogenic P. acnes by at least about 40%. In certain embodiments,the probiotic reduces growth (or re-growth) of the pathogenic P. acnesby at least about 50%. In certain embodiments, the probiotic reducesgrowth (or re-growth) of the pathogenic P. acnes by at least about 60%.In certain embodiments, the probiotic reduces growth (or re-growth) ofthe pathogenic P. acnes by at least about 70%. In certain embodiments,the probiotic reduces growth (or re-growth) of the pathogenic P. acnesby at least about 2-fold. In certain embodiments, the probiotic reducesgrowth (or re-growth) of the pathogenic P. acnes by at least about3-fold. In certain embodiments, the probiotic reduces growth (orre-growth) of the pathogenic P. acnes by at least about 5-fold. Incertain embodiments, the probiotic reduces growth (or re-growth) of thepathogenic P. acnes by at least about 10-fold. Inhibition or reductionof growth (or re-growth) of the pathogenic P. acnes may be assessed inan in vitro assay, either in liquid culture or on solid media.

In some embodiments, the probiotic comprises at least one healthy P.acnes strain. In some embodiments, the probiotic comprises not more thanone healthy P. acnes strain. In some embodiments, the probioticcomprises at least two healthy P. acnes strains. In some embodiments,the at least one healthy P. acnes strain is not a strain of P. acnessubsp. acnes. In some embodiments, the probiotic comprises at least onehealthy P. avidum strain. In some embodiments, the probiotic comprisesnot more than one healthy P. avidum strain. In some embodiments, theprobiotic comprises at least two healthy P. avidum strains. In someembodiments, the probiotic comprises at least one healthy P. granulosumstrain. In some embodiments, the probiotic comprises not more than onehealthy P. granulosum strain. In some embodiments, the probioticcomprises at least two healthy P. granulosum strains. In someembodiments, the probiotic comprises at least one healthy P. acnessubsp. defendens strain. In some embodiments, the probiotic comprisesnot more than one healthy P. acnes subsp. defendens strain. In someembodiments, the probiotic comprises at least two healthy P. acnessubsp. defendens strains.

P. acnes strains may be characterized by a ribotype (RT). Ribotypes aredefined, for example, as in Fitz-Gibbon et al., J. InvestigativeDermatology 133:2152-60 (2013). A ribotype can be determined by thenucleic acid sequence of the strain's 16S ribosomal subunit. In certainembodiments, the probiotic comprises healthy P. acnes of a ribotypeselected from at least one of the following ribotypes of RT1, RT2, RT3,RT4, RT5, RT7, RT8, RT9, or RT10. In certain embodiments, the probioticcomprises healthy P. acnes of a ribotype selected from at least one ofthe following ribotypes of RT1, RT2, RT3, RT7, RT8, RT9, or RT10. Incertain embodiments, the probiotic comprises healthy P. acnes of aribotype selected from RT1 and RT2. In some instances, the probioticdoes not comprise a P. acnes strain of ribotype RT6. In some instances,the probiotic does not comprise a P. acnes strain of a ribotype selectedfrom RT3, RT4, RT5 and RT6. In some instances, the probiotic does notcomprise a P. acnes strain of ribotype RT6. In some instances, theprobiotic does not comprise a P. acnes strain of a ribotype selectedfrom RT3, RT4, and RT5. In some embodiments, compositions disclosedherein comprise a strain of P. acnes of ribotype RT1. In someembodiments, compositions disclosed herein comprise a strain of P. acnesof ribotype RT2. In some embodiments, compositions disclosed hereincomprise a strain of P. acnes of ribotype RT3. In some embodiments,compositions disclosed herein comprise a strain of P. acnes of ribotypeRT4. In some embodiments, compositions disclosed herein comprise astrain of P. acnes of ribotype RT5. In some embodiments, compositionsdisclosed herein comprise a strain of P. acnes of ribotype RT6. In someembodiments, compositions disclosed herein comprise a strain of P. acnesof ribotype RT7. In some embodiments, compositions disclosed hereincomprise a strain of P. acnes of ribotype RT8. In some embodiments,compositions disclosed herein comprise a strain of P. acnes of ribotypeRT9. In some embodiments, compositions disclosed herein comprise astrain of P. acnes of ribotype RT10. In certain embodiments, theprobiotic comprises a strain of P. acnes of a ribotype selected from atleast one of RT1, RT2, and RT3. In certain embodiments, the probioticcomprises a P. acnes strain of ribotype RT1. In certain embodiments, theprobiotic comprises a P. acnes strain of ribotype RT2. In certainembodiments, the probiotic comprises a P. acnes strain of ribotype RT3.In certain embodiments, the probiotic comprises a P. acnes strain ofribotype RT3. In certain embodiments, the probiotic does not comprise anRT6 ribotype.

In certain embodiments, the probiotic does not comprise a strain with anucleic acid having a sequence that is 95%, 97%, 98%, 99% or 100%homologous to a sequence selected from SEQ ID NO: 51, SEQ ID NO: 52, SEQID NO: 53, and SEQ ID NO: 54. In certain embodiments, the probiotic doesnot comprise a strain with a nucleic acid having a sequence that is morethan 50% homologous to a sequence selected from SEQ ID NO: 51, SEQ IDNO: 52, SEQ ID NO: 53, and SEQ ID NO: 54. In certain embodiments, theprobiotic does not comprise a strain with a nucleic acid having asequence selected from SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53.

In certain embodiments, probiotics disclosed herein comprise a pluralityof microbes of different ribotypes. In certain embodiments, theplurality of microbes is a mixture of two or more P. acnes strains ofdifferent ribotypes. In certain embodiments, the probiotic comprises afirst strain of P. acnes of ribotype RT1 and a second strain of P. acnesof ribotype RT2. In certain embodiments, the probiotic comprises a firststrain of P. acnes of ribotype RT1 and a second strain of P. acnes ofribotype RT3. In certain embodiments, the probiotic comprises a firststrain of P. acnes of ribotype RT1 and a second strain of P. acnes isnot ribotype RT6. In certain embodiments, the probiotic comprises afirst strain of P. acnes of ribotype RT2 and a second strain of P. acnesof ribotype RT3. In certain embodiments, the probiotic comprises a firststrain of P. acnes of ribotype RT2 and a second strain of P. acnes isnot ribotype RT6. In certain embodiments, the probiotic comprises afirst strain of P. acnes of ribotype RT2 and a second strain of P. acnesof ribotype RT3. In certain embodiments, the probiotic consistsessentially of a first strain of P. acnes of ribotype RT1 and a secondstrain of P. acnes of ribotype RT2. In certain embodiments, theprobiotic consists essentially of a first strain of P. acnes of ribotypeRT1 and a second strain of P. acnes of ribotype RT3. In certainembodiments, the probiotic consists essentially of a first strain of P.acnes of ribotype RT1 and a second strain of P. acnes is not ribotypeRT6. In certain embodiments, the probiotic consists essentially of afirst strain of P. acnes of ribotype RT2 and a second strain of P. acnesof ribotype RT3. In certain embodiments, the probiotic consistsessentially of a first strain of P. acnes of ribotype RT2 and a secondstrain of P. acnes is not ribotype RT6. In certain embodiments, theprobiotic consists essentially of a first strain of P. acnes of ribotypeRT2 and a second strain of P. acnes of ribotype RT3. In someembodiments, the first strain of P. acnes and the second strain of P.acnes are provided separately. In some embodiments, the first strain ofP. acnes and second strain of P. acnes are mixed.

In some embodiments, probiotics disclosed herein comprise ahealth-associated P. acnes strain that is ribotype RT1, deoR-positive,type II lipase-positive, does not comprise Cas5, and has less than 5%pIMPLE plasmid. In some embodiments, deoR-positive means that the straincomprises a nucleic acid encoding deoR. In some embodiments,deoR-positive means that the strain comprises a deoR protein. In someembodiments, type II lipase-positive means that the strain comprises anucleic acid encoding type II lipase. In some embodiments, type IIlipase-positive means that the strain comprises a type II lipaseprotein. In some embodiments, the strain does not comprise a nucleicacid encoding a Cas 5 protein. In some embodiments, probiotics disclosedherein comprise a health-associated P. acnes strain that is ribotypeRT2, deoR-positive, type II lipase-positive, Cas5-positive and has lessthan 5% pIMPLE plasmid.

In certain embodiments, the probiotic is a plurality of microbes ofdifferent ribotypes. In certain embodiments, the plurality of microbescomprises a mixture of three or more P. acnes strains of differentribotypes. In certain embodiments, the different ribotypes are RT1, RT2,and RT3. In certain embodiments, the different ribotypes are RT2, RT3,and not RT6. In certain embodiments, the different ribotypes are RT1,RT2, and not RT6. In certain embodiments, the different ribotypes areRT1, RT3, and not RT6. In certain embodiments, the mixture consistsessentially of three P. acnes strains, wherein the three P. acnesstrains are of ribotypes RT1, RT2, and RT3. In certain embodiments, themixture consists essentially of three P. acnes strains, wherein thethree P. acnes strains are of ribotypes RT2, RT3, and not RT6. Incertain embodiments, the mixture consists essentially of three P. acnesstrains, wherein the three P. acnes strains are of ribotypes RT1, RT2,and not RT6. In certain embodiments, the mixture consists essentially ofthree P. acnes strains, wherein the three P. acnes strains are ofribotypes RT1, RT3, and not RT6.

In some embodiments, probiotics disclosed herein comprise at least onehealth-associated strain of P. acnes, wherein the health-associatedstrain of P. acnes has a ribotype of RT1 or RT2. In some embodiments,probiotics disclosed herein comprise at least two health-associatedstrains of P. acnes, wherein a first health-associated strain of P.acnes has a ribotype of RT1 and a second health-associated strain of P.acnes has a ribotype of RT2. In some embodiments, probiotics disclosedherein do not comprise a strain of P. acnes, other than ahealth-associated strain of P. acnes disclosed herein that has aribotype selected from RT1 and RT2. In some embodiments, the probioticdoes not comprise a strain of P. acnes that has a ribotype RT6. In someembodiments, the probiotic does not comprise a strain of P. acnes thatcomprises a nucleic acid encoding a DNA binding response regulator or aphosphoglycerate kinase, as described herein. In some embodiments, theprobiotic comprises a strain of P. acnes comprising a nucleic acidencoding an ATP binding cassette transporter, as described herein. Insome embodiments, the probiotic does not comprise a strain of P. acnesthat expresses DNA binding response regulator or phosphoglyceratekinase, as described herein. In some embodiments, the probioticcomprises a strain of P. acnes that expresses an ATP binding cassettetransporter, as described herein.

In some embodiments, probiotics disclosed herein comprise at least onestrain of bacteria that can be identified by a genetic signature. Thegenetic signature can be described as one or more genes that are atleast present, and optionally expressed, in a strain of bacteria. Theone or more genes may comprise a gene encoding a deoxyribose operonrepressor (deoR). The one or more genes may encode a type I lipase. Theone or more genes may encode a type II lipase. The one or more genes mayencode Cas 5. In some instances, the one or more genes do not comprise agene encoding a deoxyribose operon repressor (gene abbreviated deoR,protein abbreviated herein as deoR). In some instances, the one or moregenes do not comprise a gene encoding a type I lipase. In someinstances, the one or more genes do not comprise a gene encoding a typeII lipase. In some instances, the one or more genes do not comprise agene encoding a Cas5 protein.

In some embodiments, probiotics disclosed herein comprise at least onestrain of bacteria expressing a type II lipase. In some embodiments,probiotics disclosed herein comprise at least one strain of bacteriaexpressing a deoR and a type II lipase. In some embodiments, probioticsdisclosed herein comprise at least one strain of bacteria expressing aCas5 and a type II lipase. In some embodiments, probiotics disclosedherein comprise at least one strain of bacteria expressing a deoR and atype II lipase and a Cas5.

In some embodiments, compositions disclosed herein comprise at least onestrain of bacteria, wherein less than about 25% of a number of readsalign per number of reads tested when the reads from sequencing thestrain are aligned to a pIMPLE plasmid. In some embodiments,compositions disclosed herein comprise at least one strain of bacteria,wherein less than about 20% of a number of reads align per number ofreads tested when the reads from sequencing the strain are aligned to apIMPLE plasmid. In some embodiments, compositions disclosed hereincomprise at least one strain of bacteria, wherein less than about 15% ofa number of reads align per number of reads tested when the reads fromsequencing the strain are aligned to a pIMPLE plasmid. In someembodiments, compositions disclosed herein comprise at least one strainof bacteria, wherein less than about 10% of a number of reads align pernumber of reads tested when the reads from sequencing the strain arealigned to a pIMPLE plasmid. In some embodiments, compositions disclosedherein comprise at least one strain of bacteria, wherein less than about9% of a number of reads align per number of reads tested when the readsfrom sequencing the strain are aligned to a pIMPLE plasmid. In someembodiments, compositions disclosed herein comprise at least one strainof bacteria, wherein less than about 8% of a number of reads align pernumber of reads tested when the reads from sequencing the strain arealigned to a pIMPLE plasmid. In some embodiments, compositions disclosedherein comprise at least one strain of bacteria, wherein less than about7% of a number of reads align per number of reads tested when the readsfrom sequencing the strain are aligned to a pIMPLE plasmid. In someembodiments, compositions disclosed herein comprise at least one strainof bacteria, wherein less than about 6% of a number of reads align pernumber of reads tested when the reads from sequencing the strain arealigned to a pIMPLE plasmid. In some embodiments, compositions disclosedherein comprise at least one strain of bacteria, wherein less than about5% of a number of reads align per number of reads tested when the readsfrom sequencing the strain are aligned to a pIMPLE plasmid. In someembodiments, compositions disclosed herein comprise at least one strainof bacteria, wherein less than about 4% of a number of reads align pernumber of reads tested when the reads from sequencing the strain arealigned to a pIMPLE plasmid. In some embodiments, compositions disclosedherein comprise at least one strain of bacteria, wherein less than about3% of a number of reads align per number of reads tested when the readsfrom sequencing the strain are aligned to a pIMPLE plasmid. In someembodiments, compositions disclosed herein comprise at least one strainof bacteria, wherein less than about 2% of a number of reads align pernumber of reads tested when the reads from sequencing the strain arealigned to a pIMPLE plasmid. In some embodiments, compositions disclosedherein comprise at least one strain of bacteria, wherein less than about1% of a number of reads align per number of reads tested when the readsfrom sequencing the strain are aligned to a pIMPLE plasmid. In someembodiments, compositions disclosed herein comprise at least one strainof bacteria, wherein less than about 0.5% of a number of reads align pernumber of reads tested when the reads from sequencing the strain arealigned to a pIMPLE plasmid.

In some embodiments, the composition comprises a strain of bacteria thatis ribotype RT1, expresses type I lipase, and does not express deoR andCas5, and wherein less than 5% of a number of reads align to pIMPLEplasmid per number of reads tested from whole genome sequencing of thestrain. In some embodiments, the composition comprises a strain ofbacteria that is ribotype RT1, expresses deoR and type I lipase, anddoes not express Cas5, and wherein less than 5% of a number of readsalign to pIMPLE plasmid per number of reads tested from whole genomesequencing of the strain. In some embodiments, the composition comprisesa strain of bacteria that is ribotype RT1, expresses deoR and type IIlipase, and does not express Cas5, and wherein less than 5% of a numberof reads align to pIMPLE plasmid per number of reads tested from wholegenome sequencing of the strain. In some embodiments, the compositioncomprises a strain of bacteria that is ribotype RT2, expresses deoR,type II lipase, and Cas5, and wherein less than 5% of a number of readsalign to pIMPLE plasmid per number of reads tested from whole genomesequencing of the strain. In some embodiments, the composition comprisesa strain of bacteria that is ribotype RT4 and expresses type I lipase,but not deoR. In some embodiments, the composition comprises a strain ofbacteria that is not ribotype RT6, expresses deoR, type II lipase, andCas5, and wherein less than 5% of a number of reads align to pIMPLEplasmid per number of reads tested from whole genome sequencing of thestrain.

In some embodiments, the composition comprises a strain of bacteria thatis ribotype RT1, comprises a nucleic acid encoding type I lipase, anddoes not comprises a nucleic acid encoding deoR or Cas5, and whereinless than 5% of a number of reads align to pIMPLE plasmid per number ofreads tested from whole genome sequencing of the strain. In someembodiments, the composition comprises a strain of bacteria that isribotype RT1, comprises at least one nucleic acid encoding deoR and typeI lipase, does not comprise a nucleic acid encoding Cas5, and whereinless than 5% of a number of reads align to pIMPLE plasmid per number ofreads tested from whole genome sequencing of the strain. In someembodiments, the composition comprises a strain of bacteria that isribotype RT1, a nucleic acid encoding deoR and type II lipase, does notcomprise a nucleic acid encoding Cas5, and wherein less than 5% of anumber of reads align to pIMPLE plasmid per number of reads tested fromwhole genome sequencing of the strain. In some embodiments, thecomposition comprises a strain of bacteria that is ribotype RT2,comprises at least one nucleic acid encoding deoR, type II lipase, andCas5, and wherein less than 5% of a number of reads align to pIMPLEplasmid per number of reads tested from whole genome sequencing of thestrain. In some embodiments, the composition comprises a strain ofbacteria that is ribotype RT4 and comprises a nucleic acid encoding typeI lipase, but does not comprise a nucleic acid encoding deoR. In someembodiments, the composition comprises a strain of bacteria that is notribotype RT6, comprises at least one nucleic acid encoding deoR, type IIlipase, and Cas5, and wherein less than 5% of a number of reads align topIMPLE plasmid per number of reads tested from whole genome sequencingof the strain.

Table 1 below provides a summary of non-limiting examples of P. acnesbacteria, or populations of bacteria comprising P. acnes bacteria, thatcan be distinguished by analysis of different genetic markers. The +symbol indicates the presence of deoR or Cas5 (or nucleic acids encodingdeoR or Cas5) in the columns labeled deoR and Cas5, respectively. The −symbol indicates absence of deoR or Cas5 (or nucleic acids encoding deoRor Cas5) in the columns labeled deoR and Cas5, respectively. % pIMPLEplasmid refers to the number of reads aligned/number of reads testedwhen bacteria is sequenced for pIMPLE plasmid.

TABLE 1 Sequences of P. acnes genetic elements. % Cas pIMPLE ABCExemplary Group RT deoR Lipase 5 plasmid XP DBRR PGK strains A 1 − I −<5% + − − B 1 + I − <5% + − − C 1 + II − <5% + − − HP3A11 D 2 + II +<5% + − − HP4G1, HP5G4 E 4 − I − >1% + − − HL045PA1 F 5 − I − >1% + − −HL043PA1 G 6 + II + >5% − + + HL110PA3, HL110PA4 ABC XP = ATP bindingcassette transporter DBRR = DNA binding response regulator PGK =phosphoglycerate kinase

In certain embodiments, the composition comprises at least one strain ofa P. acnes microbe that corresponds to group A of Table 1. In certainembodiments, the composition comprises at least one strain of a P. acnesmicrobe that corresponds to group B of Table 1. In certain embodiments,the composition comprises at least one strain of a P. acnes microbe thatcorresponds to group C of Table 1. In certain embodiments, thecomposition comprises at least one strain of a P. acnes microbe thatcorresponds to group D of Table 1.

In certain embodiments, the composition comprises at least one strain ofa P. acnes microbe that corresponds to groups A, B, C or D of Table 1.In certain embodiments, the composition comprises at least two strainsof a P. acnes microbe that correspond to groups A, B, C or D of Table 1.In certain embodiments, the composition comprises at least three strainsof a P. acnes microbe that correspond to groups A, B, C or D of Table 1.In certain embodiments, the composition comprises at least four strainsof a P. acnes microbe that correspond to groups A, B, C or D of Table 1.In certain embodiments, the composition comprises at least five strainsof a P. acnes microbe that correspond to groups A, B, C, or D of Table1.

In some embodiments, the composition does not comprise a strain of P.acnes that corresponds to group E of Table 1. In some embodiments, thecomposition does not comprise a strain of P. acnes that corresponds togroup F of Table 1. In some embodiments, the composition does notcomprise a strain of P. acnes that corresponds to group G of Table 1.

In some embodiments, the composition comprises at least one strain of P.acnes that corresponds to group A of Table 1, but does not comprise astrain of P. acnes that corresponds to groups E, F or G of Table 1. Insome embodiments, the composition comprises at least one strain of P.acnes that corresponds to group B of Table 1, but does not comprise astrain of P. acnes that corresponds to groups E, F or G of Table 1. Insome embodiments, the composition comprises at least one strain of P.acnes that corresponds to group C of Table 1, but does not comprise astrain of P. acnes that corresponds to groups E, F or G of Table 1. Insome embodiments, the composition comprises at least one strain of P.acnes that corresponds to group D of Table 1, but does not comprise astrain of P. acnes that corresponds to groups E, F or G of Table 1. Insome embodiments, the composition comprises at least one strain of P.acnes that corresponds to group C of Table 1 and at least one strain ofP. acnes that corresponds to group D of Table 1, but does not comprise astrain of P. acnes that corresponds to groups E, F or G of Table 1.

Health-Associated Microbes

Provided herein are compositions for treating and preventing skindisorders, wherein the compositions comprise a health-associatedmicrobe. Generally, the term, “health-associated microbe,” as usedherein, refers to a microbe that is more prevalent in healthy orindividuals free of a skin disease than in individuals diagnosed withthe skin disease. In some embodiments, health-associated microbesdisclosed herein are associated with desirable or optimal oral health.In some embodiments, health-associated microbes disclosed herein areassociated with desirable or optimal gastrointestinal health.

Health-associated microbes include probiotics described herein.Health-associated microbes include healthy P. acnes described herein. Insome embodiments, health-associated microbes are microbes that canreplace at least a portion of pathogenic microbes. In some embodiments,health-associated microbes are microbes that can alter a microbiome toincrease a percentage of health associated strains. In some embodiments,health-associated microbes inhibit the growth of pathogenic microbes ordisease associated microbes. In some embodiments, health-associatedmicrobes out-compete pathogenic or disease associated microbes. Incertain embodiments, the skin disorder is selected from at least one ofacne vulgaris (acne), eczema, seborrheic dermatitis, psoriasis, orrosacea. In some embodiments, the skin disorder is acne.

In certain embodiments, health-associated microbes disclosed herein areassociated with desirable health, optimal health or improved healthrelative to the health of a subject with a disease, disorder orcondition disclosed herein. Desirable health, optimal health or improvedhealth may be characterized as free of a condition, disorder or disease.Desirable health, optimal health or improved health may be characterizedas free of one or more symptoms of a condition, disorder or disease.Desirable health, optimal health or improved health may be characterizedas free of all symptoms of a condition, disorder or disease. Desirablehealth, optimal health or improved health may be characterized asimproved health relative to health with a disease, disorder orcondition. In certain embodiments, the health-associated microbe isassociated with optimal, desirable or improved skin health. In certainembodiments, the health-associated microbe is associated with optimal,desirable or improved oral health. In certain embodiments, thehealth-associated microbe is associated with optimal, desirable orimproved digestive health. In certain embodiments, the health-associatedmicrobe is a P. acnes strain associated with skin health, oral health,digestive health, or any combination thereof, that is optimal, desirableor improved relative to respective health associated with a condition,disorder or disease.

In certain embodiments, there is a statistically significant differencein the presence of the health-associated microbe on the skin of anindividual free of a disease when compared to an individual with thedisease. In certain embodiments, there is at least about a 10% greaterquantity of a health-associated microbe on the skin of an individualfree of a disease when compared to an individual with the disease. Incertain embodiments, there is at least about a 50% greater quantity of ahealth-associated microbe on the skin of an individual free of a diseasewhen compared to an individual with the disease. In certain embodiments,there is at least about a 100% greater quantity of a health-associatedmicrobe on the skin of an individual free of a disease when compared toan individual with the disease. In certain embodiments, there is atleast about a 2-fold greater presence of the health-associated microbeon the skin of an individual free of a disease when compared to anindividual with the disease. In certain embodiments, there is at leastabout a 3-fold greater presence of the health-associated microbe on theskin of an individual free of a disease when compared to an individualwith the disease. In certain embodiments, there is at least about a5-fold greater presence of the health-associated microbe on the skin ofan individual free of a disease when compared to an individual with thedisease. In certain embodiments, there is at least about a 10-foldgreater presence of the health-associated microbe on the skin of anindividual free of a disease when compared to an individual with thedisease.

In certain embodiments, the health-associated microbe is an isolatedspecies of bacteria. In certain embodiments, the health-associatedmicrobe is a purified species of bacteria. In certain embodiments, thehealth-associated microbe is an isolated and purified species ofbacteria. In certain embodiments, the health-associated microbe is anisolated strain of bacteria. In certain embodiments, thehealth-associated microbe is a purified strain of bacteria. In certainembodiments, the health-associated microbe is an isolated and purifiedstrain of bacteria. In certain embodiments, the health-associatedmicrobe is an isolated species of Propionibacterium. In certainembodiments, the health-associated microbe is a purified species ofPropionibacterium. In certain embodiments, the health-associated microbeis an isolated and purified species of Propionibacterium. In certainembodiments, the health-associated microbe is an isolated strain of P.acnes. In certain embodiments, the health-associated microbe is apurified strain of P. acnes. In certain embodiments, thehealth-associated microbe is an isolated and purified strain of P.acnes.

As described herein, some strains of P. acnes are associated with acneand some strains of P. acnes are associated with skin free of acne ordisease. These P. acnes strains can be differentiated at the geneticlevel by using nucleic acid sequence determination methods known in theart such as PCR, restriction mapping, Sanger sequencing, andnext-generation sequencing. In some instances, a health-associatedmicrobe disclosed herein is beneficial for the treatment of a specificskin disorder, but not all skin disorders. In some instances, ahealth-associated microbe disclosed herein is beneficial for thetreatment of a plurality of skin disorder, but not all skin disorders.In some instances, a health-associated microbe disclosed herein isbeneficial for the treatment any skin disorder. By way of non-limitingexample, a health-associated microbe disclosed herein may be beneficialonly for acne, but not for eczema, seborrheic dermatitis, or psoriasis.In another instance, a health-associated microbe disclosed herein isbeneficial only for eczema, but not for acne, seborrheic dermatitis, orpsoriasis. In another instance, a health-associated microbe disclosedherein is beneficial only for psoriasis, but not for acne, seborrheicdermatitis, or eczema. In another instance, a health-associated microbedisclosed herein is beneficial only for seborrheic dermatitis, but notfor psoriasis, acne, or eczema. In some instances, a health-associatedmicrobe disclosed herein is beneficial for eczema, acne and psoriasis.In some instances, a health-associated microbe disclosed herein isbeneficial for acne and a condition selected from eczema, seborrheicdermatitis. In some instances, a health-associated microbe disclosedherein is beneficial for eczema, seborrheic dermatitis, acne andpsoriasis.

In certain embodiments, compositions disclosed herein comprise at leastone health-associated microbe, wherein the health-associated microbe isa strain of P. acnes or bacteria that is associated with healthy ornormal skin. In certain embodiments, compositions disclosed hereincomprise at least one health-associated microbe, wherein thehealth-associated microbe is a strain of P. acnes or bacteria thatproduces low levels of inflammatory mediators when incubated with asubject's own keratinocytes or pooled keratinocytes from multiplesubjects.

In certain embodiments, compositions comprise an isolatedPropionibacterium strain. In some embodiments the isolatedPropionibacterium strain is a purified strain. In certain embodiments,compositions comprise a mixture of about 2 to about 10 isolatedPropionibacterium strains. In certain embodiments, compositions comprisea mixture of about 3 to about 8 isolated Propionibacterium strains. Incertain embodiments, compositions comprise a mixture of about 2 to about5 isolated Propionibacterium strains. In certain embodiments,compositions comprise a mixture of about 3 to about 6 isolatedPropionibacterium strains. In certain embodiments, the isolatedPropionibacterium strain is isolated based on its phylotype or ribotype.Propionibacterium strains are disclosed throughout the instantspecification.

In certain embodiments, compositions consist essentially of an isolatedPropionibacterium strain and a pharmaceutically acceptable excipient orbiological stabilizer. In certain embodiments, compositions consistessentially of two isolated Propionibacterium strains and apharmaceutically acceptable excipient or biological stabilizer. In someembodiments the isolated Propionibacterium strain is a purified strain.In certain embodiments, compositions consist essentially of about 2 toabout 10 isolated Propionibacterium strains, and a pharmaceuticallyacceptable excipient or biological stabilizer disclosed herein. Incertain embodiments, compositions consist essentially of about 3 toabout 8 isolated Propionibacterium strains, and a pharmaceuticallyacceptable excipient or biological stabilizer disclosed herein. Incertain embodiments, compositions consist essentially of about 2 toabout 5 isolated Propionibacterium strains, and a pharmaceuticallyacceptable excipient or biological stabilizer disclosed herein. Incertain embodiments, compositions consist essentially of about 3 toabout 6 isolated Propionibacterium strains, and a pharmaceuticallyacceptable excipient or biological stabilizer disclosed herein. Incertain embodiments, the isolated strain is isolated based on itsphylotype or ribotype. Exemplary Propionibacterium strains and apharmaceutically acceptable excipient or biological stabilizer aredescribed throughout the instant specification.

In certain embodiments, compositions consist essentially of an isolatedPropionibacterium strain, a pharmaceutically acceptable excipient orbiological stabilizer, and at least one additional active ingredientdisclosed herein. In certain embodiments, compositions consistessentially of two isolated Propionibacterium strains, apharmaceutically acceptable excipient or biological stabilizer, and atleast one additional active ingredient disclosed herein. In someembodiments the isolated Propionibacterium strain is a purified strain.In certain embodiments, compositions consist essentially of about 2 toabout 10 isolated Propionibacterium strains, a pharmaceuticallyacceptable excipient or biological stabilizer, and at least oneadditional active ingredient disclosed herein. In certain embodiments,compositions consist essentially of about 3 to about 8 isolatedPropionibacterium strains, a pharmaceutically acceptable excipient orbiological stabilizer, and at least one additional active ingredientdisclosed herein. In certain embodiments, compositions consistessentially of about 2 to about 5 isolated Propionibacterium strains, apharmaceutically acceptable excipient or biological stabilizer, and atleast one additional active ingredient disclosed herein. In certainembodiments, compositions consist essentially of about 3 to about 6isolated Propionibacterium strains, a pharmaceutically acceptableexcipient or biological stabilizer, and at least one additional activeingredient disclosed herein. In certain embodiments, the isolated strainis isolated based on its phylotype or ribotype. ExemplaryPropionibacterium strains and a pharmaceutically acceptable excipient orbiological stabilizer are described throughout the instantspecification.

In certain embodiments, compositions comprise an isolated P. acnesstrain. In some embodiments the isolated P. acnes strain is a purifiedstrain. In certain embodiments, compositions comprise a mixture of about2 to about 10 isolated P. acnes strains. In certain embodiments,compositions comprise a mixture of about 3 to about 8 isolated P. acnesstrains. In certain embodiments, compositions comprise a mixture ofabout 2 to about 5 isolated P. acnes strains. In certain embodiments,compositions comprise a mixture of about 3 to about 6 isolated P. acnesstrains. In certain embodiments, the isolated P. acnes strain isisolated based on its phylotype or ribotype.

In certain embodiments, compositions consist essentially of an isolatedP. acnes strain and a pharmaceutically acceptable excipient orbiological stabilizer. In certain embodiments, compositions consistessentially of two isolated P. acnes strains and a pharmaceuticallyacceptable excipient or biological stabilizer. In some embodiments theisolated P. acnes strain is a purified strain. In certain embodiments,compositions consist essentially of about 2 to about 10 isolated P.acnes strains and a pharmaceutically acceptable excipient or biologicalstabilizer disclosed herein. In certain embodiments, compositionsconsist essentially of about 3 to about 8 isolated P. acnes strains anda pharmaceutically acceptable excipient or biological stabilizerdisclosed herein. In certain embodiments, compositions consistessentially of about 2 to about 5 isolated P. acnes strains and apharmaceutically acceptable excipient or biological stabilizer disclosedherein. In certain embodiments, compositions consist essentially ofabout 3 to about 6 isolated P. acnes strains and a pharmaceuticallyacceptable excipient or biological stabilizer disclosed herein. Incertain embodiments, the isolated strain is isolated based on itsphylotype or ribotype. Exemplary P. acnes strains and a pharmaceuticallyacceptable excipient or biological stabilizer are described throughoutthe instant specification.

In certain embodiments, compositions consist essentially of an isolatedP. acnes strain, a pharmaceutically acceptable excipient or biologicalstabilizer, and at least one additional active ingredient disclosedherein. In certain embodiments, compositions consist essentially of twoisolated P. acnes strains, a pharmaceutically acceptable excipient orbiological stabilizer, and at least one additional active ingredientdisclosed herein. In some embodiments the isolated P. acnes strain is apurified strain. In certain embodiments, compositions consistessentially of about 2 to about 10 isolated P. acnes strains, apharmaceutically acceptable excipient or biological stabilizer, and atleast one additional active ingredient disclosed herein. In certainembodiments, compositions consist essentially of about 3 to about 8isolated P. acnes strain, a pharmaceutically acceptable excipient orbiological stabilizer, and at least one additional active ingredientdisclosed herein. In certain embodiments, compositions consistessentially of about 2 to about 5 isolated P. acnes strains and apharmaceutically acceptable excipient or biological stabilizer disclosedherein, a pharmaceutically acceptable excipient or biologicalstabilizer, and at least one additional active ingredient disclosedherein. In certain embodiments, compositions consist essentially ofabout 3 to about 6 isolated P. acnes strain, a pharmaceuticallyacceptable excipient or biological stabilizer, and at least oneadditional active ingredient disclosed herein. In certain embodiments,the isolated strain is isolated based on its phylotype or ribotype.Exemplary P. acnes strains and a pharmaceutically acceptable excipientor biological stabilizer are described throughout the instantspecification.

In certain embodiments, compositions disclosed herein comprise at leastone P. acnes strain having a health-associated phylotype. In certainembodiments, the health-associated phylotype is selected from type I,type II, and type III. In some embodiments, compositions disclosedherein comprise at least two P. acnes strains having health-associatedphylotypes, wherein the health-associated phylotypes are a combinationof type I, type II, and type III. In certain embodiments, the type Iphylotype is selected from type IA, type IB, and type IC. In certainembodiments, the type IA phylotype is selected from type IA₁ and typeIA₂. Strains can be phylotyped as in McDowell et al. (PLoS ONE 8(9):e70897 (2013)).

In some embodiments, compositions disclosed herein comprise acombination of health-associated microbes, wherein the health-associatedmicrobes comprise a combination of healthy strains of P. acnes. In someembodiments, combinations of healthy strains of P. acnes comprise acombination of strains of P. acnes of a plurality of ribotypes. In someembodiments, the plurality of ribotypes comprises at least two ribotypesselected from RT1, RT2, RT3, RT7, RT8, RT9, and RT10. In someembodiments, the plurality of ribotypes comprises at least two ribotypesselected from RT1, RT2 and RT3. In certain embodiments, the plurality ofribotypes comprises at least two ribotypes selected from RT1, RT2, RT3and not RT6. In certain embodiments, the plurality of ribotypescomprises ribotypes selected from RT1 and RT2. In certain embodiments,the plurality of ribotypes comprises ribotypes selected from RT1 andRT3. In certain embodiments, the plurality of ribotypes comprisesribotypes selected from RT2 and RT3. In certain embodiments, theplurality of ribotypes comprises RT1, but not RT6. In certainembodiments, the plurality of ribotypes comprises RT2, but not RT6.

In some embodiments, compositions disclosed herein comprise acombination of health-associated microbes, wherein the health-associatedmicrobes comprise a combination of healthy strains of P. acnes. In someembodiments, the combination comprises a first strain of P. acnes and asecond strain of P. acnes. In some embodiments, the first strain of P.acnes is of a first ribotype and a second strain of P. acnes is of asecond ribotype. In some embodiments, the first ribotype and the secondribotype are the same. In some embodiments, the first ribotype and thesecond ribotype are different. In some embodiments, the first ribotypeis RT1 and the second ribotype is RT1. In some embodiments, the firstribotype is RT2 and the second ribotype is RT2. In some embodiments, thefirst ribotype is RT1 and the second ribotype is RT2. In someembodiments, the first ribotype is RT1 and the second ribotype is RT3.In some embodiments, the first ribotype is RT2 and the second ribotypeis RT3. In some embodiments, the first ribotype is RT1 and the secondribotype is not RT6. In some embodiments, the first ribotype is RT2 andthe second ribotype is not RT6. In some embodiments, the first ribotypeis RT3 and the second ribotype is not RT6.

In some embodiments, compositions disclosed herein comprise healthystrains of P. acnes, and do not comprise any other type of microbe orbacteria. In some embodiments, health-associated microbes disclosedherein comprise at least one health-associated strain of P. acnes,wherein the health-associated strain of P. acnes has a ribotype of RT1or RT2. In some embodiments, health-associated microbes disclosed hereindo not comprise a strain of P. acnes, other than a health-associatedstrain of P. acnes disclosed herein that has a ribotype selected fromRT1 and RT2. In some embodiments, the health-associated microbes do notcomprise a strain of P. acnes that has a ribotype RT6. In someembodiments, the health-associated microbes do not comprise a strain ofP. acnes that expresses DNA binding response regulator orphosphoglycerate kinase, as described herein. In some embodiments, thehealth-associated microbes comprise a strain of P. acnes that expressesan ATP binding cassette transporter, as described herein.

In certain embodiments, the health-associated microbe does not comprisea strain with a sequence that is 95%, 97%, 98%, 99% or 100% homologousto a sequence selected from SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53,and SEQ ID NO: 54. In certain embodiments, the health-associated microbedoes not comprise a strain with a sequence that is more than 50%homologous to a sequence selected from SEQ ID NO: 51, SEQ ID NO: 52, SEQID NO: 53, and SEQ ID NO: 54. In certain embodiments, thehealth-associated microbe does not comprise a strain with a sequenceselected from SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53.

In certain embodiments, compositions disclosed herein comprise ahealth-associated microbe, wherein the health-associated microbe isLactobacillus reuteri (referred to herein as L. reuteri), or a strainthereof. In certain embodiments, compositions disclosed herein compriseat least one L. reuteri strain selected from Korean Collection for TypeCultures (KCTC) deposited strains, such as KCTC 3679, KCTC 3594, KCTC3678, and any combination thereof.

In certain embodiments, compositions disclosed herein comprise ahealth-associated microbe, wherein the health-associated microbe isStaphylococcus epidermidis (S. epidermidis). In certain embodiments,compositions disclosed herein comprise at least one S. epidermidisstrain selected from 14.1.R1, AS1, AU 10, AU16, AU21, AU23, AU24, AU35,AU36, AU39, AU40, AU 44, AU48, AU53, AU60, AU73, AU81, FS1, G53, IS2,and a combination thereof.

Selected, Transformed, or Engineered Bacteria

In certain embodiments, the compositions described herein comprise oneor more strains of bacteria that is selected, transformed or engineeredwith a gene or gene mutation that is beneficial for a skin disorder.Thus, the bacteria have been transformed into a “non-pathogenic” form,or a health-associated form from a disease-associated form. In certainembodiments, a gene that contributes to pathogenesis of a skin disorderis deleted or mutated to inactivate or reduce the corresponding geneproduct. In certain embodiments, a gene that reduces the pathogenesis ofa skin disorder is added, or mutated to activate or increase levels ofthe corresponding gene product. In certain embodiments, the bacteria aregrown and selected from culture or selected from healthy disease freeindividuals.

In certain embodiments, selected, transformed, or engineered bacteriaare to be delivered as a probiotic via compositions and methodsdisclosed herein. In certain embodiments, selected, transformed, orengineered bacteria disclosed herein comprise a gene encoding adeoxyribose operon repressor (deoR). In certain embodiments, selected,transformed, or engineered bacteria disclosed herein express adeoxyribose operon repressor. In certain embodiments, selected,transformed, or engineered bacteria disclosed herein comprise a geneencoding a Type II lipase. In certain embodiments, selected,transformed, or engineered bacteria disclosed herein express Type IIlipase. By way of non-limiting example, the Type II lipase may be aglycerol-ester hydrolase B (GehB). In certain embodiments, selected,transformed, or engineered bacteria disclosed herein do not comprise agene encoding Type I lipase. In certain embodiments, selected,transformed, or engineered bacteria disclosed herein do not express aType I lipase. By way of non-limiting example, the type I lipase may bea glycerol-ester hydrolase A (GehA). In certain embodiments, selected,transformed, or engineered bacteria do not comprise a pIMPLE plasmid. Incertain embodiments, selected, transformed, or engineered bacteriadisclosed herein comprise a gene encoding an ABC transporter. In certainembodiments, selected, transformed, or engineered bacteria express anABC transporter. In certain embodiments, selected, transformed, orengineered bacteria disclosed herein do not comprise a gene encoding aphosphoglycerate kinase. In certain embodiments, selected, transformed,or engineered bacteria do not comprise a phosphoglycerate kinase. Incertain embodiments, selected, transformed, or engineered bacteriadisclosed herein do not comprise a gene encoding a DNA binding responseregulator. In certain embodiments, selected, transformed, or engineeredbacteria do not comprise a DNA binding response regulator.

In certain embodiments, selected, transformed, or engineered bacteriadisclosed herein do not express a dermatin-sulfate adhesin (e.g., DSA1,DSA2). In certain embodiments, selected, transformed, or engineeredbacteria disclosed herein do comprise a nucleic acid encoding adermatin-sulfate adhesin (e.g., DSA1, DSA2). The absence or deletion ofdermatin-sulfate adhesins may disable adhesion of microbes tokeratinocytes.

In certain embodiments, selected, transformed, or engineered bacteriadisclosed herein express a hyaluronidase. In some embodiments, thehyaluronidase is a hyaluronidase expressed by a Group B Streptococcusstrain of bacteria. In certain embodiments, selected, transformed, orengineered bacteria disclosed herein do not express a hyaluronidase. Incertain embodiments, selected, transformed, or engineered bacteriadisclosed herein comprise a nucleic acid encoding a hyaluronidase. Insome embodiments, the nucleic acid encodes a hyaluronidase expressed bya Group B Streptococcus strain of bacteria. In certain embodiments,selected, transformed, or engineered bacteria disclosed herein do notcomprise a nucleic acid encoding a hyaluronidase. In certainembodiments, a strain of bacteria that is selected, transformed, orengineered bacteria is present or has increased expression of ahyaluronidase gene relative to the strain of bacteria when it is notselected, transformed, or engineered. In certain embodiments, a strainof bacteria that is selected, transformed, or engineered bacteria ispresent or has increased hyaluronidase activity relative to the strainof bacteria when it is not selected, transformed, or engineered. Incertain embodiments, a strain of bacteria that is selected, transformed,or engineered bacteria is present or has reduced hyaluronidase activityrelative to the strain of bacteria when it is not selected, transformed,or engineered. In certain embodiments, selected, transformed, orengineered bacteria disclosed herein lack a hyaluronidase gene.

In certain embodiments, selected, transformed, or engineered bacteriadisclosed herein have reduced transposase 2 enzyme activity. In certainembodiments, selected, transformed, or engineered bacteria disclosedherein lack transposase 2 enzyme activity. In certain embodiments, aselected, transformed, or engineered strain of bacteria disclosed hereinhas reduced activity relative to the strain when it is not selected,transformed, or engineered, respectively.

In certain embodiments, selected, transformed, or engineered bacteriadisclosed herein confer an antibiotic sensitivity to macrolide andtetracycline antibiotics. In certain embodiments, selected, transformed,or engineered bacteria disclosed herein have an absence or deletion of athiopeptide encoding island, respectively. In certain embodiments,selected, transformed, or engineered bacteria disclosed herein have apresence or addition of a tyrosine decarboxylase island (which increasesintracellular pH under stress to tolerate acidic environments),respectively. In certain embodiments, selected, transformed, orengineered bacteria disclosed herein have an ability to metabolizegelatin.

In certain embodiments, selected, transformed, or engineered bacteriacomprise selected, transformed, or engineered S. epidermis,respectively. In certain embodiments, the selected, transformed, orengineered bacteria comprise selected, transformed, or engineered P.acnes.

In certain embodiments, the bacteria are transformed using recombinantDNA techniques known in the art. In certain embodiments, the bacteriaare transformed by growing bacteria under selective pressure to acquireor lose a gene, gene product, or expression thereof. In a certainembodiment, the bacteria are transformed using CRISPR technology. In acertain embodiment, the bacteria are transformed using homologousrecombination.

In certain embodiments, the selected, transformed, or engineeredbacteria comprise a selected, transformed, or engineered P. acnesstrain. In certain embodiments, the selected, transformed, or engineeredbacteria comprise a selected, transformed, or engineered P. acnesstrain, wherein the selected, transformed, or engineered P. acnes strainhas a ribotype selected from RT1, RT2, RT3, RT4, RT5, RT7, RT8, RT9, andRT10. In certain embodiments, the selected, transformed, or engineeredbacteria comprise a selected, transformed, or engineered P. acnesstrain, wherein the selected, transformed, or engineered P. acnes strainhas a ribotype selected from RT1, RT2, RT3, RT7, RT8, RT9, and RT10. Incertain embodiments, the selected, transformed, or engineered bacteriacomprise a selected, transformed, or engineered P. acnes strain, whereinthe selected, transformed, or engineered P. acnes strain has a ribotypeselected from RT1, RT2, RT3, RT7, RT8, RT9, and RT10. In certainembodiments, the selected, transformed, or engineered bacteria comprisea selected, transformed, or engineered P. acnes strain, wherein theselected, transformed, or engineered P. acnes strain has a ribotypeselected from RT1, RT2, RT3, and not RT6. In certain embodiments, theselected, transformed, or engineered bacteria comprise a selected,transformed, or engineered P. acnes strain, wherein the selected,transformed, or engineered P. acnes strain has a ribotype selected fromRT1 and RT2. In certain embodiments, the selected, transformed, orengineered bacteria comprise a selected, transformed, or engineered P.acnes strain, wherein the selected, transformed, or engineered P. acnesstrain has a ribotype of RT1. In certain embodiments, the selected,transformed, or engineered bacteria comprise a selected, transformed, orengineered P. acnes strain, wherein the selected, transformed, orengineered P. acnes strain has a ribotype of RT2. In certainembodiments, the selected, transformed, or engineered bacteria are anRT1 strain of P. acnes. In certain embodiments, the selected,transformed, or engineered bacteria are an RT2 strain of P. acnes. Incertain embodiments, the selected, transformed, or engineered bacteriaare an RT3 strain of P. acnes. In certain embodiments, the selected,transformed, or engineered bacteria are not an RT6 strain of P. acnes.

Markers

Disclosed herein are compositions that comprise probiotics andhealth-associated microbes. Probiotics and health-associated microbesdisclosed herein generally comprise at least one strain of bacteria,wherein the at least one strain of bacteria exhibits a health-associatedpresence, health-associated absence or health-associated expressionlevel of at least one marker. In some instances, health-associatedexpression of the at least one marker is a lack of expression. In someinstances, health-associated expression of the at least one marker isexpression that is low as compared to expression of the at least onemarker in a reference strain. In some instances, the reference strain isa pathogenic strain. In some instances, the reference strain is not ahealth-associated strain. In some instances, health-associatedexpression of the at least one marker is expression that is high ascompared to expression of the at least one marker in a reference strain.

In some embodiments, the marker is a nucleic acid. In some embodiments,the nucleic acid comprises a gene encoding the marker or a portionthereof. In some embodiments, the nucleic acid is a gene encoding themarker or a portion thereof. In some embodiments, the marker is aprotein. In some embodiments, the marker is a peptide (e.g., less thanor equal to 100 amino acids). In some embodiments, the marker is not anucleic acid or a protein. Non-limiting examples of a marker thatneither comprises a nucleic acid or protein include glycans and lipids.

Exemplary markers of health-associated microbes disclosed hereininclude, but are not limited to, a deoxyribose operon repressor, aCRISPR associated protein (Cas), a lipase, an ATP binding cassettetransporter, a DNA binding response regulator, a phosphoglyceratekinase, dermatin-sulfate adhesin, and hyaluronidase. In some instances,the at least one strain of bacteria comprises a plasmid. In someinstances, presence or absence of the plasmid is a marker. By way ofnon-limiting example, the plasmid may be a pIMPLE plasmid disclosedherein. As further described herein, presence of a deoR, a type IIlipase, an ABC transporter, or a Cas5, or a combination thereof, isgenerally associated with probiotics and health-associated microbesdisclosed herein. In contrast, probiotics and health-associated microbesdisclosed herein are generally associated with an absence or lowexpression of a pIMPLE plasmid, a type I lipase, a DNA binding responseregulator, a phosphoglycerate kinase, or dermatin-sulfate adhesin, or acombination thereof. However, it would be understood to one of skill inthe art that nature presents exceptions to such generalities. Therefore,expression patterns of these markers that are alternative or contrary tothose described herein are contemplated as well. Compositions comprisingone or more strains characterized by such markers are furthercharacterized herein, including the description as follows.

deoR

In some embodiments, the marker is a deoxyribose operon repressor (deoR)protein. In some embodiments, the marker is a nucleic acid encoding adeoxyribose operon repressor (deoR). In some embodiments, the deoR is adeoR family transcriptional regulator expressed in Propionibacteriumacnes subsp. defendens (ATCC 11828, GenBank: AER05724.1). In certainembodiments, the at least one strain of bacteria has been selected,transformed, or engineered to acquire the presence of the deoR. Incertain embodiments, the deoR has a sequence that is at least 80%homologous to SEQ ID NO: 1. In certain embodiments, the deoR has asequence that is at least 90% homologous to SEQ ID NO: 1. In certainembodiments, the deoR has a sequence that is at least 95% homologous toSEQ ID NO: 1. In certain embodiments, the deoR has a sequence that is atleast 97% homologous to SEQ ID NO: 1. In certain embodiments, the deoRhas a sequence that is at least 98% homologous to SEQ ID NO: 1. Incertain embodiments, the deoR has a sequence that is at least 99%homologous to SEQ ID NO: 1. In certain embodiments, the deoR has asequence that is 100% homologous to SEQ ID NO: 1. In certainembodiments, the at least one strain of bacteria has greater expressionor activity of a deoxyribose operon repressor than a reference strain(e.g., pathogenic strain, not a health-associated strain). In certainembodiments, the at least one strain has at least about 1.5-fold, atleast about 2-fold, at least about 3-fold, at least about 5-fold or atleast about 10-fold greater expression or activity of the deoxyriboseoperon repressor as compared to the reference strain.

pIMPLE Plasmid

In some embodiments, the marker is a pIMPLE plasmid. In someembodiments, the marker is an absence of a pIMPLE plasmid. In someembodiments, the marker is a low percentage of a pIMPLE plasmid (e.g.,<10%). In some embodiments, compositions disclosed herein comprise atleast one strain of bacteria, wherein the at least one strain ofbacteria does not comprise a pIMPLE plasmid. In certain embodiments, thepIMPLE plasmid has a sequence that is at least about 80% homologous toSEQ ID NO: 2. In certain embodiments, the pIMPLE plasmid has a sequencethat is at least about 90% homologous to SEQ ID NO: 2. In certainembodiments, the pIMPLE plasmid has a sequence that is at least about95% homologous to SEQ ID NO: 2. In certain embodiments, the pIMPLEplasmid has a sequence that is at least about 97% homologous to SEQ IDNO: 2. In certain embodiments, the pIMPLE plasmid has a sequence that isat least about 98% homologous to SEQ ID NO: 2. In certain embodiments,the pIMPLE plasmid has a sequence that is at least about 99% homologousto SEQ ID NO: 2. In certain embodiments, the pIMPLE plasmid has asequence that is 100% homologous to SEQ ID NO: 2. In certainembodiments, a plasmid with at least 80%, 90%, 95%, 98%, 99%, or 100%homology to SEQ ID NO: 2 is partially or completely deleted from the atleast one strain of bacteria. In certain embodiments, a plasmid with atleast 80%, 90%, 95%, 98%, 99%, or 100% homology to SEQ ID NO: 2 isdisrupted by an insertion of one or more nucleotides or a introductionof a frameshift mutation in the a selected, transformed, or engineeredstrain of bacteria. In certain embodiments, the at least one strain ofbacteria contains portions of a complete pIMPLE plasmid (SEQ ID NO: 2).In certain embodiments, the at least one strain of bacteria may compriseless than about 25%, 20%, 15%, 14%, 13%, 12%, 11%, 10%, 9%, 8%, 7%, 6%of the complete pIMPLE sequence set forth in SEQ ID NO: 2. In certainembodiments, the at least one strain of bacteria does not comprise aspecific portion of the pIMPLE plasmid that is present in an RT6 strainor any other disease associated strain. In certain embodiments, the atleast one strain of bacteria comprises a low copy number of a pIMPLEplasmid (SEQ ID NO: 2). In certain embodiments, the at least one strainof bacteria comprises less than 5 copies of pIMPLE plasmid per bacterialgenome. In certain embodiments, the at least one strain of bacteriacomprises less than 4 copies of pIMPLE plasmid per bacterial genome. Incertain embodiments, the at least one strain of bacteria comprises lessthan 3 copies of pIMPLE plasmid per bacterial genome. In certainembodiments, the at least one strain of bacteria comprises less than 2copies of pIMPLE plasmid per bacterial genome. In certain embodiments,the at least one strain of bacteria comprises 1 copy of pIMPLE plasmidper bacterial genome. In certain embodiments, the at least one strain ofbacteria comprises a low percentage of pIMPLE plasmid (SEQ ID NO: 2). Incertain embodiments, the bacteria comprise less than about 15%, 14%,13%, 12%, 11%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1% pIMPLE plasmid.In certain embodiments, the at least one strain of bacteria comprisesless than about 1.0%, 0.9%, 0.8%, 0.7%, 0.6%, 0.5%, 0.4%, 0.3%, 0.2%,0.1% pIMPLE plasmid. pIMPLE plasmid percentage can be determined bynext-generation sequencing of P. acnes bacteria, as % reads aligned. Incertain embodiments, the pIMPLE percentage is percentage of totalsequencing reads that align to pIMPLE from HL096PA1 (an RT5).

Lipases

In some embodiments, the marker is a lipase. In some embodiments, themarker is a nucleic acid encoding a lipase. In some embodiments, themarker is an absence of a nucleic acid encoding a lipase. In someembodiments, compositions disclosed herein comprise a strain of bacteriathat expresses a lipase. In some embodiments, the lipase is Type Ilipase. In some embodiments, the lipase is Type II lipase. In someembodiments, the compositions disclosed herein comprise a strain ofbacteria that does not express a lipase. In some embodiments, thecompositions disclosed herein comprise a strain of bacteria that doesnot express a Type I lipase. In some embodiments, the compositionsdisclosed herein comprise a strain of bacteria that does not express aType II lipase. In some embodiments, the strain of bacteria comprises anucleic acid encoding a Type II lipase. Type I lipase and Type IIlipase, as described herein, may be encoded by a similar nucleic acid.For example, a gene encoding Type I lipase will encode a Type II lipaseupon a 6 bp deletion in the intergenic region and a single basedeletion, the latter causing a frameshift that creates premature STOPcodon, see, e.g., FIG. 7.

Type I Lipase

In some embodiments, the marker is a Type I lipase. In some embodiments,compositions disclosed herein comprise at least one strain of bacteria,wherein the at least one strain of bacteria does not express a Type Ilipase. In some embodiments, compositions disclosed herein comprise atleast one strain of bacteria, wherein the at least one strain ofbacteria does not comprise a nucleic acid encoding a Type I lipase. Incertain embodiments, compositions disclosed herein comprise at least onestrain of bacteria, wherein the at least one strain of bacteria has beenselected, transformed, or engineered for an absence of Type I lipaseexpression or activity. In certain embodiments, compositions disclosedherein comprise at least one strain of bacteria, wherein the at leastone strain of bacteria has been selected, transformed, or engineered forthe presence of Type I lipase expression or activity. In certainembodiments, compositions disclosed herein comprise at least one strainof bacteria, wherein the strain has been selected, transformed, orengineered for lower expression or activity of Type I lipase relative toa reference strain (e.g., pathogenic strain, not a health-associatedstrain). In certain embodiments, at least one strain of bacteria has atleast about 1.5-fold lower expression or activity of Type I lipasecompared to the reference strain. In certain embodiments, at least onestrain of bacteria has at least about 2-fold lower expression oractivity of Type I lipase compared to the reference strain. In certainembodiments, at least one strain of bacteria has at least about 3-foldlower expression or activity of Type I lipase compared to the referencestrain. In certain embodiments, at least one strain of bacteria has atleast about 5-fold lower expression or activity of Type I lipasecompared to the reference strain. In certain embodiments, at least onestrain of bacteria has at least about 10-fold lower expression oractivity of Type I lipase compared to the reference strain.

In some embodiments, compositions disclosed herein comprise at least onestrain of bacteria, wherein the at least one strain of bacteriaexpresses a Type I lipase. In certain embodiments, compositionsdisclosed herein comprise at least one strain of bacteria, wherein theat least one strain of bacteria has been selected, transformed, orengineered for the presence of Type I lipase expression or activity. Incertain embodiments, compositions disclosed herein comprise at least onestrain of bacteria, wherein the strain has been selected, transformed,or engineered for greater expression or activity of Type I lipaserelative to the reference strain.

In some embodiments, at least a portion of the Type I lipase is encodedby a sequence of SEQ ID NO: 10. In some embodiments, at least a portionof the Type I lipase is encoded by a sequence that is at least 80%homology to SEQ ID NO: 10. In some embodiments, at least a portion ofthe Type I lipase is encoded by a sequence that is at least 90% homologyto SEQ ID NO: 10. In some embodiments, at least a portion of the Type Ilipase is encoded by a sequence that is at least 95% homology to SEQ IDNO: 10. In some embodiments, at least a portion of the Type I lipase isencoded by a sequence that is at least 97% homology to SEQ ID NO: 10. Insome embodiments, at least a portion of the Type I lipase is encoded bya sequence that is at least 98% homology to SEQ ID NO: 10. In someembodiments, at least a portion of the Type I lipase is encoded by asequence that is at least 99% homology to SEQ ID NO: 10. In someembodiments, at least a portion of the Type I lipase is encoded by asequence that is at least 80% homology to SEQ ID NO: 10. In someembodiments, at least a portion of the Type I lipase is encoded by asequence of SEQ ID NO: 60. In some embodiments, at least a portion ofthe Type I lipase is encoded by a sequence that is at least 80% homologyto SEQ ID NO: 60. In some embodiments, at least a portion of the Type Ilipase is encoded by a sequence that is at least 90% homology to SEQ IDNO: 60. In some embodiments, at least a portion of the Type I lipase isencoded by a sequence that is at least 95% homology to SEQ ID NO: 60. Insome embodiments, at least a portion of the Type I lipase is encoded bya sequence that is at least 97% homology to SEQ ID NO: 60. In someembodiments, at least a portion of the Type I lipase is encoded by asequence that is at least 98% homology to SEQ ID NO: 60. In someembodiments, at least a portion of the Type I lipase is encoded by asequence that is at least 99% homology to SEQ ID NO: 60. In someembodiments, at least a portion of the Type I lipase is encoded by asequence that is at least 80% homology to SEQ ID NO: 60.

In certain embodiments, a nucleic acid with at least 80%, 90%, 95%, 98%,99%, or 100% homology to SEQ ID NO: 10 is partially or completelydeleted from the at least one strain. In certain embodiments, thenucleic acid is deleted by at least about 5%, at least about 10%, atleast about 15%, at least about 20%, at least about 25%, at least about30%, at least about 35%, at least about 40%, at least about 45%, atleast about 50%, at least about 55%, at least about 60%, at least about65%, at least about 70%, at least about 75%, at least about 80%, atleast about 85%, at least about 90%, at least about 95% or more from the3 prime end of the nucleic acid. In certain embodiments, the nucleicacid is deleted by at least about 5%, at least about 10%, at least about15%, at least about 20%, at least about 25%, at least about 30%, atleast about 35%, at least about 40%, at least about 45%, at least about50%, at least about 55%, at least about 60%, at least about 65%, atleast about 70%, at least about 75%, at least about 80%, at least about85%, at least about 90%, at least about 95% or more from the 5 prime endof the nucleic acid.

In certain embodiments, a nucleic acid with at least 80%, 90%, 95%, 98%,99%, or 100% homology to SEQ ID NO: 10 is disrupted by an insertion ofone or more nucleotides or a introduction of a frameshift mutation inthe at least one strain. In certain embodiments, at least about 5%, atleast about 10%, at least about 15%, at least about 20%, at least about25%, at least about 30%, at least about 35%, at least about 40%, atleast about 45%, at least about 50%, at least about 55%, at least about60%, at least about 65%, at least about 70%, at least about 75%, atleast about 80%, at least about 85%, at least about 90%, or at leastabout 95% of the nucleic acid with at least 80%, 90%, 95%, 98%, 99%, or100% homology to SEQ ID NO: 10 is disrupted.

Type II Lipase

In some embodiments, compositions disclosed herein comprise at least onestrain of bacteria, wherein the at least one strain of bacteriaexpresses a Type II lipase. A non-limiting example of a Type II lipaseis Lipase ADE00051, HMPREF0675_4856. In some embodiments, compositionsdisclosed herein comprise at least one strain of bacteria, wherein theat least one strain of bacteria comprises a nucleic acid encoding a TypeII lipase. In certain embodiments, the at least one strain of bacteriahas been selected, transformed, or engineered to express a Type IIlipase. In certain embodiments, the at least one strain of bacteria hasat least about 1.5-fold greater expression or activity of Type II lipasecompared to a reference strain (e.g., pathogenic strain, not ahealth-associated strain). In certain embodiments, the at least onestrain of bacteria has at least about 2-fold greater expression oractivity of Type II lipase compared to the reference strain. In certainembodiments, the at least one strain of bacteria has at least about3-fold greater expression or activity of Type II lipase compared to thereference strain. In certain embodiments, the at least one strain ofbacteria has at least about 5-fold greater expression or activity ofType II lipase compared to the reference strain. In certain embodiments,the at least one strain of bacteria has at least about 10-fold greaterexpression or activity of Type II lipase compared to the referencestrain.

In some embodiments, at least a portion of the type II lipase isexpressed from a nucleic acid comprising SEQ ID NO.: 61. SEQ ID NO.: 61is found in the complete circular genome of Propionibacterium acnes ATCC11828 and starts at position 390,423 of ATCC 11828. The followingsubsequent positions are in reference to the first nucleotide of SEQ IDNO.: 61. The lipase coding sequence is bases 22-1032, referred to hereinas ADE0051, HMPREF0675_4856, and SEQ ID NO.: 3. Bases 1-21 is anintergenic region. Type II Lipase has a Gin position 7 and an A inposition 16. In some embodiments, at least a portion of the type Ilipase is expressed from a nucleic acid comprising SEQ ID NO.: 60. Incontrast, relative to SEQ ID NO. 61, SEQ ID NO. 60 has a 6 bp sequenceTAGATA inserted between base pairs 1 and 2, an A in position 7, a G inposition 16, and a G between base pairs 145 and 146. SEQ ID NO.: 60 andSEQ ID NO.: 61 are shown in Table 8. FIG. 7 also illustrates thedifferences between sequences encoding Type I lipase and Type II lipase.

In certain embodiments, at least a portion of the Type II lipase isencoded by a nucleic acid with at least about 90% homology to SEQ ID NO:3. In certain embodiments, at least a portion of the Type II lipase isencoded by a nucleic acid with at least about 95% homology to SEQ ID NO:3. In certain embodiments, at least a portion of the Type II lipase isencoded by a nucleic acid with at least about 97% homology to SEQ ID NO:3. In certain embodiments, at least a portion of the Type II lipase isencoded by a nucleic acid with at least about 97% homology to SEQ ID NO:3. In certain embodiments, at least a portion of the Type II lipase isencoded by a nucleic acid with at least about 99% homology to SEQ ID NO:3. In certain embodiments, at least a portion of the Type II lipase isencoded by a nucleic acid with 100% homology to SEQ ID NO: 3. In certainembodiments, at least a portion of the Type II lipase is encoded by anucleic acid with at least about 90% homology to SEQ ID NO: 61. Incertain embodiments, at least a portion of the Type II lipase is encodedby a nucleic acid with at least about 95% homology to SEQ ID NO: 61. Incertain embodiments, at least a portion of the Type II lipase is encodedby a nucleic acid with at least about 97% homology to SEQ ID NO: 61. Incertain embodiments, at least a portion of the Type II lipase is encodedby a nucleic acid with at least about 97% homology to SEQ ID NO: 61. Incertain embodiments, at least a portion of the Type II lipase is encodedby a nucleic acid with at least about 99% homology to SEQ ID NO: 61. Incertain embodiments, at least a portion of the Type II lipase is encodedby a nucleic acid with 100% homology to SEQ ID NO: 61.

CRISPR/Cas5

In some embodiments, compositions disclosed herein comprise at least onestrain of bacteria, wherein the at least one strain of bacteriacomprises a CRISPR locus or a portion of a CRISPR locus. In someembodiments, compositions disclosed herein comprise at least one strainof bacteria, wherein the at least one strain of bacteria expresses aCRISPR-associated protein (Cas). By way of non-limiting example, theCRISPR-associated proteins include Cas5, Cas9, Cpf1, Cas3, Cas8a, Cas8b,Cas8c, Cas10d, Cse1, Cse2, Csy1, Csy2, Csy3, GSU0054, Cas10, Csm2, Cmr5,Cas10, Csx11, Csx10, Csf1, Csn2, Cas4, C2c1, C2c3, and C2c2.

In some embodiments, compositions disclosed herein comprise at least onestrain of bacteria, wherein the at least one strain of bacteriaexpresses a Cas5. In some embodiments, compositions disclosed hereincomprise at least one strain of bacteria, wherein the at least onestrain of bacteria comprises a nucleic acid encoding a Cas5. In certainembodiments, the at least one strain of bacteria has been selected,transformed, or engineered to express a Cas5. In certain embodiments,the at least one strain of bacteria has at least about 1.5-fold greaterexpression or activity of Cas5 compared to a reference strain (e.g.,pathogenic strain, not a health-associated strain). In certainembodiments, the at least one strain of bacteria has at least about2-fold greater expression or activity of Cas5 compared to the referencestrain. In certain embodiments, the at least one strain of bacteria hasat least about 3-fold greater expression or activity of Cas5 compared tothe reference strain. In certain embodiments, the at least one strain ofbacteria has at least about 5-fold greater expression or activity ofCas5 compared to the reference strain. In certain embodiments, the atleast one strain of bacteria has at least about 10-fold greaterexpression or activity of Cas5 compared to the reference strain.

In some instances, the at least one strain of bacteria expresses Cas5.In some embodiments, a strain of P. acnes is characterized as ahealth-associated P. acnes or a disease-associated P. acnes based on thepresence of Cas5. In some embodiments, Cas5 is found in P. acnes strainATCC 11828. In some embodiments, Cas5 is encoded by a sequence as setforth in SEQ ID NO: 8. In some embodiments, Cas5 is encoded by asequence that is at least about 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%,95%, 96%, 97%, 98%, 99%, or 100% homologous to SEQ ID NO: 8. In someembodiments, Cas5 is encoded by a sequence that is about 70%, 80%, 85%,90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequenceidentity to SEQ ID NO: 8. In some embodiments, Cas5 is encoded by asequence that is about 95% homologous to SEQ ID NO: 8. In someembodiments, Cas5 is encoded by a sequence that is about 97% homologousto SEQ ID NO: 8. In some embodiments, Cas5 is encoded by a sequence thatis about 99% homologous to SEQ ID NO: 8. In some embodiments, Cas5 isencoded by a sequence that is about 100% homologous to SEQ ID NO: 8.

In some instances, the at least one strain of bacteria comprises anucleic acid encoding Cas5, wherein the nucleic acid comprises at leastabout 10, at least about 20, at least about 30, at least about 40, atleast about 50, at least about 60, at least about 70, at least about 80,at least about 90, at least about 100, at least about 110, at leastabout 120, at least about 130, at least about 140, at least about 150,at least about 160, at least about 170, at least about 180, at leastabout 190, at least about 200, at least about 210, at least about 220,at least about 230, at least about 240, at least about 250, at leastabout 260, at least about 270, at least about 280, at least about 290,at least about 300, at least about 310, at least about 320, at leastabout 330, at least about 340, at least about 350, at least about 360,at least about 370, at least about 380, at least about 390, at leastabout 400, at least about 410, at least about 420, at least about 430,at least about 440, at least about 450, at least about 460, at leastabout 470, at least about 480, at least about 490, at least about 500,at least about 550, at least about 650, at least about 700, or more thanabout 700 consecutive bases of SEQ ID NO: 8. In some instances, the atleast one strain of bacteria comprises a nucleic acid encoding Cas5,wherein the nucleic acid comprises about 10, about 20, about 30, about40, about 50, about 60, about 70, about 80, about 90, about 100, about110, about 120, about 130, about 140, about 150, about 160 about 170,about 180, about 190, about 200, about 210, about 220, about 230, about240, about 250, about 260, about 270, about 280, about 290, about 300,about 310, about 320, about 330, about 340, about 350, about 360, about370, about 380, about 390, about 400, about 410, about 420, about 430,about 440, about 450, about 460, about 470, about 480, about 490, about500, about 550, about 650, about 700, or more than about 700 consecutivebases of SEQ ID NO: 8.

ABC Transporter

In some embodiments, compositions disclosed herein comprise at least onestrain of bacteria, wherein the at least one strain of bacteriacomprises an ATP-binding cassette transporter. In certain embodiments,the at least one strain of bacteria comprises a nucleic acid encoding anATP-binding cassette transporter (ABC transporter). In certainembodiments, the at least one strain of bacteria is selected forexpression or overexpression of a nucleic acid encoding an ABCtransporter. In certain embodiments, the at least one strain of bacteriais selected for increased activity of an ABC transporter. In certainembodiments, the at least one strain of bacteria is selected for thepresence of a nucleic acid encoding an ABC transporter. In certainembodiments, the at least one strain of bacteria is transformed foroverexpression of a nucleic acid encoding an ABC transporter. In certainembodiments, the at least one strain of bacteria is transformed forincreased activity of an ABC transporter. In certain embodiments, the atleast one strain of bacteria is transformed for the presence of anucleic acid encoding an ABC transporter. In certain embodiments, the atleast one strain of bacteria is engineered for overexpression of anucleic acid encoding an ABC transporter. In certain embodiments, the atleast one strain of bacteria is engineered for increased activity of anABC transporter. In certain embodiments, the at least one strain ofbacteria is engineered for the presence of a nucleic acid encoding anABC transporter. In some embodiments, the ABC transporter is a portionof a known ABC transporter. In some embodiments, the ABC transporter isa portion of a known ABC transporter, wherein the portion of the knownABC transporter can perform an activity of the known ABC transporter. Insome embodiments, the ABC transporter is a portion of a known ABCtransporter, wherein the portion of the known ABC transporter canperform an enzymatic activity of the known ABC transporter. In someembodiments, the ABC transporter is a portion of a known ABCtransporter, wherein the portion of the known ABC transporter canperform a transport activity of the known ABC transporter.

In certain embodiments, the at least one strain has at least about1.5-fold greater expression or activity of ABC transporter compared to areference strain (e.g., pathogenic strain, not a health-associatedstrain). In certain embodiments, the at least one strain has at leastabout 2-fold greater expression or activity of ABC transporter comparedto the reference strain. In certain embodiments, the at least one strainhas at least about 3-fold greater expression or activity of ABCtransporter compared to the reference strain. In certain embodiments,the at least one strain has at least about 5-fold greater expression oractivity of ABC transporter compared to the reference strain. In certainembodiments, the at least one strain has at least about 10-fold greaterexpression or activity of ABC transporter compared to the referencestrain.

In some embodiments, ABC transporters disclosed herein are encoded by asequence of SEQ ID NO.: 6 or a sequence that is homologous to SEQ IDNO.: 6. In some embodiments, the ABC transporter is encoded by asequence that is at least about 80% homologous to SEQ ID NO: 6. In someembodiments, the ABC transporter is encoded by a sequence that is atleast about 90% homologous to SEQ ID NO: 6. In some embodiments, the ABCtransporter is encoded by a sequence that is at least about 95%homologous to SEQ ID NO: 6. In some embodiments, the ABC transporter isencoded by a sequence that is at least about 96% homologous to SEQ IDNO: 6. In some embodiments, the ABC transporter is encoded by a sequencethat is at least about 97% homologous to SEQ ID NO: 6. In someembodiments, the ABC transporter is encoded by a sequence that is atleast about 98% homologous to SEQ ID NO: 6. In some embodiments, the ABCtransporter is encoded by a sequence that is at least about 99%homologous to SEQ ID NO: 6. In some embodiments, the ABC transporter isencoded by a sequence that is 100% homologous to SEQ ID NO: 6. Incertain embodiments, the at least one strain is (completely orpartially) selected, transformed, or engineered with a nucleic acid thatis at least about 80%, 90%, 95%, 98%, 99%, or 100% homology to SEQ IDNO: 6 is partially or completely present in the at least one strain.

DNA Binding Response Regulator

In some embodiments, compositions disclosed herein comprise at least onestrain of bacteria, wherein the at least one strain of bacteria does notcomprise a DNA binding response regulator. In certain embodiments, theat least one strain does not comprise a nucleic acid encoding a DNAbinding response regulator. In certain embodiments, the at least onestrain has been selected for reduced expression or activity of a DNAbinding response regulator. In certain embodiments, the at least onestrain has been selected for an absence of a DNA binding responseregulator. In certain embodiments, bacteria disclosed herein have beentransformed for reduced expression or activity of a DNA binding responseregulator. In certain embodiments, bacteria disclosed herein have beentransformed for an absence of a DNA binding response regulator. Incertain embodiments, bacteria disclosed herein have been engineered forreduced expression or activity of a DNA binding response regulator. Incertain embodiments, bacteria disclosed herein have been engineered foran absence of a DNA binding response regulator.

In certain embodiments, the at least one strain of bacteria has at leastabout 1.5-fold less expression or activity of a DNA binding responseregulator relative to a reference strain (e.g., pathogenic strain, not ahealth-associated strain). In certain embodiments, the at least onestrain has at least about 2-fold less expression or activity of a DNAbinding response regulator relative to the reference strain. In certainembodiments, the at least one strain has at least about 3-fold lessexpression or activity of a DNA binding response regulator relative tothe reference strain. In certain embodiments, the at least one strainhas at least about 5-fold less expression or activity of a DNA bindingresponse regulator relative to the reference strain. In certainembodiments, the at least one strain has at least about 10-fold lessexpression or activity of a DNA binding response regulator relative tothe reference strain.

In certain embodiments, the at least one strain has been selected,transformed, or engineered to remove a nucleic acid with at least 90%homology to SEQ ID NO: 7. In certain embodiments, the at least onestrain has been selected, transformed, or engineered to express anucleic acid with at least 90% homology to SEQ ID NO: 7 at a lower levelrelative to the reference strain. In certain embodiments, the at leastone strain has been selected, transformed, or engineered to remove anucleic acid with at least 95% homology to SEQ ID NO: 7. In certainembodiments, the at least one strain has been selected, transformed, orengineered to express a nucleic acid with at least 95% homology to SEQID NO: 7 at a lower level relative to the reference strain. In certainembodiments, the at least one strain has been selected, transformed, orengineered to remove a nucleic acid with at least 97% homology to SEQ IDNO: 7. In certain embodiments, the at least one strain has beenselected, transformed, or engineered to express a nucleic acid with atleast 97% homology to SEQ ID NO: 7 at a lower level relative to thereference strain. In certain embodiments, the at least one strain hasbeen selected, transformed, or engineered to remove a nucleic acid withat least 99% homology to SEQ ID NO: 7. In certain embodiments, the atleast one strain has been selected, transformed, or engineered toexpress a nucleic acid with at least 99% homology to SEQ ID NO: 7 at alower level relative to the reference strain. In certain embodiments,the at least one strain has been selected, transformed, or engineered toremove a nucleic acid with 100% homology to SEQ ID NO: 7. In certainembodiments, the at least one strain has been selected, transformed, orengineered to express a nucleic acid with 100% homology to SEQ ID NO: 7at a lower level relative to the reference strain.

In certain embodiments, the at least one strain comprises a nucleic acidthat is disrupted by an insertion of one or more nucleotides or aintroduction of a frameshift mutation, wherein the nucleic acid has 80%,90%, 95%, 98%, 99%, or 100% homology to SEQ ID NO: 7, before beingdisrupted. For example, in certain embodiments, a nucleic acid with atleast 80%, 90%, 95%, 98%, 99%, or 100% homology to SEQ ID NO: 7 isdeleted by at least about 5%, at least about 10%, at least about 15%, atleast about 20%, at least about 25%, at least about 30%, at least about35%, at least about 40%, at least about 45%, at least about 50%, atleast about 55%, at least about 60%, at least about 65%, at least about70%, at least about 75%, at least about 80%, at least about 85%, atleast about 90%, at least about 95% or more from the 3 prime end of thenucleic acid. In certain embodiments, the nucleic acid with at least80%, 90%, 95%, 98%, 99%, or 100% homology to SEQ ID NO: 7 is deleted byat least about 5%, at least about 10%, at least about 15%, at leastabout 20%, at least about 25%, at least about 30%, at least about 35%,at least about 40%, at least about 45%, at least about 50%, at leastabout 55%, at least about 60%, at least about 65%, at least about 70%,at least about 75%, at least about 80%, at least about 85%, at leastabout 90%, at least about 95% or more from the 5 prime end of thenucleic acid.

Phosphoglycerate Kinase

In some embodiments, compositions disclosed herein comprise at least onestrain of bacteria, wherein the at least one strain of bacteria does notcomprise a phosphoglycerate kinase. In certain embodiments, the at leastone strain does not comprise a nucleic acid encoding a phosphoglyceratekinase. In certain embodiments, the at least one strain has beenselected for reduced expression or activity of a phosphoglyceratekinase. In certain embodiments, the at least one strain has beenselected for an absence of a phosphoglycerate kinase. In certainembodiments, bacteria disclosed herein have been transformed for reducedexpression or activity of a phosphoglycerate kinase. In certainembodiments, bacteria disclosed herein have been transformed for anabsence of a phosphoglycerate kinase. In certain embodiments, bacteriadisclosed herein have been engineered for reduced expression or activityof a phosphoglycerate kinase. In certain embodiments, bacteria disclosedherein have been engineered for an absence of a phosphoglycerate kinase.

In certain embodiments, the at least one strain of bacteria has at leastabout 1.5-fold less expression or activity of a phosphoglycerate kinaserelative to a reference strain (e.g., pathogenic strain, not ahealth-associated strain). In certain embodiments, the at least onestrain has at least about 2-fold less expression or activity of aphosphoglycerate kinase relative to the reference strain. In certainembodiments, the at least one strain has at least about 3-fold lessexpression or activity of a phosphoglycerate kinase relative to thereference strain. In certain embodiments, the at least one strain has atleast about 5-fold less expression or activity of a phosphoglyceratekinase relative to the reference strain. In certain embodiments, the atleast one strain has at least about 10-fold less expression or activityof a phosphoglycerate kinase relative to the reference strain.

In certain embodiments, the at least one strain has been selected,transformed, or engineered to remove a nucleic acid with at least 90%homology to SEQ ID NO: 9. In certain embodiments, the at least onestrain has been selected, transformed, or engineered to express anucleic acid with at least 90% homology to SEQ ID NO: 9 at a lower levelrelative to the reference strain. In certain embodiments, the at leastone strain has been selected, transformed, or engineered to remove anucleic acid with at least 95% homology to SEQ ID NO: 9. In certainembodiments, the at least one strain has been selected, transformed, orengineered to express a nucleic acid with at least 95% homology to SEQID NO: 9 at a lower level relative to the reference strain. In certainembodiments, the at least one strain has been selected, transformed, orengineered to remove a nucleic acid with at least 97% homology to SEQ IDNO: 9. In certain embodiments, the at least one strain has beenselected, transformed, or engineered to express a nucleic acid with atleast 97% homology to SEQ ID NO: 9 at a lower level relative to thereference strain. In certain embodiments, the at least one strain hasbeen selected, transformed, or engineered to remove a nucleic acid withat least 99% homology to SEQ ID NO: 9. In certain embodiments, the atleast one strain has been selected, transformed, or engineered toexpress a nucleic acid with at least 99% homology to SEQ ID NO: 9 at alower level relative to the reference strain. In certain embodiments,the at least one strain has been selected, transformed, or engineered toremove a nucleic acid with 100% homology to SEQ ID NO: 9. In certainembodiments, the at least one strain has been selected, transformed, orengineered to express a nucleic acid with 100% homology to SEQ ID NO: 9at a lower level relative to the reference strain.

In certain embodiments, the at least one strain comprises a nucleic acidthat is disrupted by an insertion of one or more nucleotides or aintroduction of a frameshift mutation, wherein the nucleic acid has 80%,90%, 95%, 98%, 99%, or 100% homology to SEQ ID NO: 9, before beingdisrupted. For example, in certain embodiments, a nucleic acid with atleast 80%, 90%, 95%, 98%, 99%, or 100% homology to SEQ ID NO: 9 isdeleted by at least about 5%, at least about 10%, at least about 15%, atleast about 20%, at least about 25%, at least about 30%, at least about35%, at least about 40%, at least about 45%, at least about 50%, atleast about 55%, at least about 60%, at least about 65%, at least about70%, at least about 75%, at least about 80%, at least about 85%, atleast about 90%, at least about 95% or more from the 3 prime end of thenucleic acid. In certain embodiments, the nucleic acid with at least80%, 90%, 95%, 98%, 99%, or 100% homology to SEQ ID NO: 9 is deleted byat least about 5%, at least about 10%, at least about 15%, at leastabout 20%, at least about 25%, at least about 30%, at least about 35%,at least about 40%, at least about 45%, at least about 50%, at leastabout 55%, at least about 60%, at least about 65%, at least about 70%,at least about 75%, at least about 80%, at least about 85%, at leastabout 90%, at least about 95% or more from the 5 prime end of thenucleic acid.

Dermatin-Sulfate Adhesin

In some embodiments, compositions disclosed herein comprise at least onestrain of bacteria, wherein the at least one strain of bacteria does notcomprise a dermatin-sulfate adhesin (DSA1 and DSA2). In certainembodiments, the at least one strain does not comprise a nucleic acidencoding a dermatin-sulfate adhesin. In certain embodiments, the atleast one strain has been selected for reduced expression or activity ofa dermatin-sulfate adhesin. In certain embodiments, the at least onestrain has been selected for an absence of a dermatin-sulfate adhesin.In certain embodiments, bacteria disclosed herein have been transformedfor reduced expression or activity of a dermatin-sulfate adhesin. Incertain embodiments, bacteria disclosed herein have been transformed foran absence of a dermatin-sulfate adhesin. In certain embodiments,bacteria disclosed herein have been engineered for reduced expression oractivity of a dermatin-sulfate adhesin. In certain embodiments, bacteriadisclosed herein have been engineered for an absence of adermatin-sulfate adhesin.

In certain embodiments, the bacteria have been selected, transformed, orengineered for lower expression or activity or deletion of adermatin-sulfate adhesin. In certain embodiments, the selected,transformed, or engineered bacteria has 1.5-fold, 2-fold, 3-fold, or10-fold less expression or activity of the DSA 1 or DSA 2 compared to areference strain. In certain embodiments, DSA1 or DSA2 is partially orcompletely deleted from the genome of the selected, transformed, orengineered, or engineered bacteria. In certain embodiments, DSA1 or DSA2is disrupted by an insertion of one or more nucleotides or anintroduction of a frameshift mutation in the genome of the selected,transformed, or engineered, or engineered bacteria.

Hyaluronidase

In some embodiments, compositions disclosed herein comprise at least onestrain of bacteria, wherein the at least one strain of bacteria does notcomprise a hyaluronidase. Hyaluronidase is also known as hyaluronatelyase (locus tag PPA_RS01930). In some embodiments, compositionsdisclosed herein comprise at least one strain of bacteria, wherein theat least one strain of bacteria does not have hyaluronidase activity. Insome embodiments, compositions disclosed herein comprise at least onestrain of bacteria, wherein the at least one strain of bacteria does notcomprise a nucleic acid encoding a hyaluronidase. In certainembodiments, the bacteria have been selected, transformed, or engineeredfor lower expression or activity of hyaluronidase relative to thebacteria before selecting, transforming or engineering, respectively.

In some embodiments, compositions disclosed herein comprise at least onestrain of bacteria, wherein the at least one strain of bacteriacomprises a hyaluronidase. In some embodiments, compositions disclosedherein comprise at least one strain of bacteria, wherein the at leastone strain of bacteria has hyaluronidase activity. In some embodiments,compositions disclosed herein comprise at least one strain of bacteria,wherein the at least one strain of bacteria has a nucleic acid encodinga hyaluronidase. In certain embodiments, the bacteria have beenselected, transformed, or engineered for greater expression or activityof hyaluronidase relative to the bacteria before selecting, transformingor engineering, respectively.

In certain embodiments, the selected, transformed, or engineeredbacteria have 1.5-fold greater or lower expression or activity ofhyaluronate lyase compared to a non-selected, transformed, or engineeredstrain. In certain embodiments, the selected, transformed, or engineeredbacteria have 2-fold greater or lower expression or activity ofhyaluronate lyase compared to a non-selected, transformed, or engineeredstrain. In certain embodiments, the selected, transformed, or engineeredbacteria have 3-fold greater or lower expression or activity ofhyaluronate lyase compared to a non-selected, transformed, or engineeredstrain. In certain embodiments, the selected, transformed, or engineeredbacteria have 5-fold greater or lower expression or activity ofhyaluronate lyase compared to a non-selected, transformed, or engineeredstrain. In certain embodiments, the selected, transformed, or engineeredbacteria have 10-fold greater or lower expression or activity ofhyaluronate lyase compared to a non-selected, transformed, or engineeredstrain. In certain embodiments, the bacteria have been selected,transformed, or engineered to acquire or express at a greater level, anucleic acid with at least 90% homology to SEQ ID NO: 4. In certainembodiments, the bacteria have been selected, transformed, or engineeredto acquire or express at a greater level, a nucleic acid with at least95% homology to SEQ ID NO: 4. In certain embodiments, the bacteria havebeen selected, transformed, or engineered to acquire or express at agreater level, a nucleic acid with at least 97% homology to SEQ ID NO:4. In certain embodiments, the bacteria have been selected, transformed,or engineered to acquire or express at higher level, a nucleic acid withat least 97% homology to SEQ ID NO: 4. In certain embodiments, thebacteria have been selected, transformed, or engineered to acquire orexpress at a higher level, a nucleic acid with at least 99% homology toSEQ ID NO: 4. In certain embodiments, the bacteria have been selected,transformed, or engineered to acquire or express at a higher level, anucleic acid with 100% homology to SEQ ID NO: 4. In certain embodiments,the bacteria is a P. acnes bacteria. In certain embodiments, a gene withat least 80%, 90%, 95%, 98%, 99%, or 100% homology to SEQ ID NO: 4 ispartially or completely deleted from the genome of the syntheticbacteria. In certain embodiments, a gene with at least 80%, 90%, 95%,98%, 99%, or 100% homology to SEQ ID NO: 4 is disrupted by an insertionof one or more nucleotides or a introduction of a frameshift mutation inthe genome of the selected, transformed, or engineered, or engineeredbacteria. In certain embodiments, the selected, transformed, orengineered or selected bacteria are deoR+, Type II lipase positive,pIMPLE negative, or CRISPR Cas5 positive. In certain embodiments, theselected, transformed, or engineered or selected bacteria comprise P.acnes of ribotype RT1 and/or RT2.

In certain embodiments, the bacteria have been selected, transformed, orengineered for lesser expression or absence of hyaluronate lyase. Incertain embodiments, the bacteria are selected, transformed, orengineered, or engineered to acquire the presence of a hyaluronidasegene. Hyaluronidase is also known as hyaluronate lyase (locus tagPPA_RS01930). In certain embodiments, the selected, transformed, orengineered, or engineered bacteria have 1.5-fold greater or lowerexpression or activity of hyaluronate lyase compared to a non-selected,transformed, or engineered strain. In certain embodiments, the selected,transformed, or engineered bacteria have 2-fold greater or lowerexpression or activity of hyaluronate lyase compared to a non-selected,transformed, or engineered strain. In certain embodiments, the selected,transformed, or engineered bacteria have 3-fold greater or lowerexpression or activity of hyaluronate lyase compared to a non-selected,transformed, or engineered strain. In certain embodiments, the selected,transformed, or engineered bacteria have 5-fold greater or lowerexpression or activity of hyaluronate lyase compared to a non-selected,transformed, or engineered strain. In certain embodiments, the selected,transformed, or engineered bacteria have 10-fold greater or lowerexpression or activity of hyaluronate lyase compared to a non-selected,transformed, or engineered strain. In certain embodiments, the bacteriahave been selected, transformed, or engineered to acquire or express ata greater level, a nucleic acid with at least 90% homology to SEQ ID NO:4. In certain embodiments, the bacteria have been selected, transformed,or engineered to acquire or express at a greater level, a nucleic acidwith at least 95% homology to SEQ ID NO: 4. In certain embodiments, thebacteria have been selected, transformed, or engineered to acquire orexpress at a greater level, a nucleic acid with at least 97% homology toSEQ ID NO: 4. In certain embodiments, the bacteria have been selected,transformed, or engineered to acquire or express at higher level, anucleic acid with at least 97% homology to SEQ ID NO: 4. In certainembodiments, the bacteria have been selected, transformed, or engineeredto acquire or express at a higher level, a nucleic acid with at least99% homology to SEQ ID NO: 4. In certain embodiments, the bacteria havebeen selected, transformed, or engineered to acquire or express at ahigher level, a nucleic acid with 100% homology to SEQ ID NO: 4. Incertain embodiments, the bacteria is a P. acnes bacteria. In certainembodiments, a nucleic acid with at least 80%, 90%, 95%, 98%, 99%, or100% homology to SEQ ID NO: 4 is partially or completely deleted fromthe genome of the synthetic bacteria. In certain embodiments, a nucleicacid with at least 80%, 90%, 95%, 98%, 99%, or 100% homology to SEQ IDNO: 4 is disrupted by an insertion of one or more nucleotides or aintroduction of a frameshift mutation in the genome of the selected,transformed, or engineered, or engineered bacteria. In certainembodiments, the selected, transformed, or engineered or selectedbacteria are deoR+, Type II lipase positive, pIMPLE negative, or CRISPRCas5 positive. In certain embodiments, the selected, transformed, orengineered or selected bacteria comprise P. acnes of ribotype RT1 and/orRT2.

Alanine Dehydrogenase

In some embodiments, compositions disclosed herein comprise at least onestrain of bacteria, wherein the at least one strain of bacteria does notcomprise an alanine dehydrogenase. In some embodiments, compositionsdisclosed herein comprise at least one strain of bacteria, wherein theat least one strain of bacteria does not have alanine dehydrogenaseactivity. In some embodiments, compositions disclosed herein comprise atleast one strain of bacteria, wherein the at least one strain ofbacteria does not comprise a nucleic acid encoding an alaninedehydrogenase. In certain embodiments, the bacteria have been selected,transformed, or engineered for lower expression or activity of alaninedehydrogenase relative to the bacteria before selection, transformationor engineering, respectively.

In certain embodiments, bacteria are selected, transformed, orengineered for the absence or deletion of a nucleic acid encodingalanine dehydrogenase or a portion thereof. In some embodiments, thealanine dehydrogenase is encoded by a sequence of SEQ ID NO: 5. In someembodiments, the alanine dehydrogenase is encoded by a sequence that isat least 80% homology to SEQ ID NO: 5. In certain embodiments, thebacteria are selected, transformed, or engineered for the absence ordeletion of an alanine dehydrogenase or a portion thereof with at least90% homology to SEQ ID NO: 5. In certain embodiments, the bacteria areselected, transformed, or engineered for the absence or deletion of analanine dehydrogenase or a portion thereof with at least 95% homology toSEQ ID NO: 5. In certain embodiments, the bacteria are selected,transformed, or engineered for the absence or deletion of an alaninedehydrogenase or a portion thereof with at least 97% homology to SEQ IDNO: 5. In certain embodiments, the bacteria are selected, transformed,or engineered for the absence or deletion of an alanine dehydrogenase ora portion thereof with at least 98% homology to SEQ ID NO: 5. In certainembodiments, the bacteria are selected, transformed, or engineered forthe absence or deletion of an alanine dehydrogenase or a portion thereofwith at least 99% homology to SEQ ID NO: 5. In certain embodiments, anucleic acid with at least 80%, 90%, 95%, 98%, 99%, or 100% homology toSEQ ID NO: 5 is partially or completely deleted from the selected,transformed, or engineered, or engineered bacteria. In certainembodiments, a nucleic acid with at least 80%, 90%, 95%, 98%, 99%, or100% homology to SEQ ID NO: 5 is disrupted by an insertion of one ormore nucleotides or a introduction of a frameshift mutation in theselected, transformed, or engineered bacteria. In certain embodiments,the nucleic acid is deleted by at least about 5%, at least about 10%, atleast about 15%, at least about 20%, at least about 25%, at least about30%, at least about 35%, at least about 40%, at least about 45%, atleast about 50%, at least about 55%, at least about 60%, at least about65%, at least about 70%, at least about 75%, at least about 80%, atleast about 85%, at least about 90%, at least about 95% or more from the3 prime end of the nucleic acid. In certain embodiments, the nucleicacid is deleted by at least about 5%, at least about 10%, at least about15%, at least about 20%, at least about 25%, at least about 30%, atleast about 35%, at least about 40%, at least about 45%, at least about50%, at least about 55%, at least about 60%, at least about 65%, atleast about 70%, at least about 75%, at least about 80%, at least about85%, at least about 90%, at least about 95% or more from the 5 prime endof the nucleic acid.

Transposase 2

In some embodiments, compositions disclosed herein comprise at least onestrain of bacteria, wherein the at least one strain of bacteria does notcomprise a transposase 2. In some embodiments, compositions disclosedherein comprise at least one strain of bacteria, wherein the at leastone strain of bacteria does not have transposase 2 activity. In someembodiments, compositions disclosed herein comprise at least one strainof bacteria, wherein the at least one strain of bacteria does notcomprise a nucleic acid encoding a transposase 2. In certainembodiments, the bacteria have been selected, transformed, or engineeredfor lower expression or activity of transposase 2 relative to thebacteria before selection, transformation or engineering, respectively.In some embodiments, compositions disclosed herein comprise at least onestrain of bacteria, wherein the at least one strain of bacteria does nothave transposase 2 activity, expresses deoR and is of ribotype RT1.

In certain embodiments, bacteria are selected, transformed, orengineered for the absence or deletion of a nucleic acid encodingtransposase 2 or a portion thereof. In some embodiments, the transposase2 is encoded by a sequence of SEQ ID NO: 48. In some embodiments, thetransposase 2 is encoded by a sequence that is at least 80% homology toSEQ ID NO: 48. In certain embodiments, the bacteria are selected,transformed, or engineered for the absence or deletion of a transposase2 or a portion thereof with at least 90% homology to SEQ ID NO: 48. Incertain embodiments, the bacteria are selected, transformed, orengineered for the absence or deletion of a transposase 2 or a portionthereof with at least 95% homology to SEQ ID NO: 48. In certainembodiments, the bacteria are selected, transformed, or engineered forthe absence or deletion of a transposase 2 or a portion thereof with atleast 97% homology to SEQ ID NO: 48. In certain embodiments, thebacteria are selected, transformed, or engineered for the absence ordeletion of a transposase 2 or a portion thereof with at least 98%homology to SEQ ID NO: 48. In certain embodiments, the bacteria areselected, transformed, or engineered for the absence or deletion of atransposase 2 or a portion thereof with at least 99% homology to SEQ IDNO: 48. In certain embodiments, a nucleic acid with at least 80%, 90%,95%, 98%, 99%, or 100% homology to SEQ ID NO: 48 is partially orcompletely deleted from the selected, transformed, or engineered, orengineered bacteria. In certain embodiments, a nucleic acid with atleast 80%, 90%, 95%, 98%, 99%, or 100% homology to SEQ ID NO: 48 isdisrupted by an insertion of one or more nucleotides or a introductionof a frameshift mutation in the selected, transformed, or engineeredbacteria. In certain embodiments, the nucleic acid is deleted by atleast about 5%, at least about 10%, at least about 15%, at least about20%, at least about 25%, at least about 30%, at least about 35%, atleast about 40%, at least about 45%, at least about 50%, at least about55%, at least about 60%, at least about 65%, at least about 70%, atleast about 75%, at least about 80%, at least about 85%, at least about90%, at least about 95% or more from the 3 prime end of the nucleicacid. In certain embodiments, the nucleic acid is deleted by at leastabout 5%, at least about 10%, at least about 15%, at least about 20%, atleast about 25%, at least about 30%, at least about 35%, at least about40%, at least about 45%, at least about 50%, at least about 55%, atleast about 60%, at least about 65%, at least about 70%, at least about75%, at least about 80%, at least about 85%, at least about 90%, atleast about 95% or more from the 5 prime end of the nucleic acid.

Additional Markers

In some embodiments, compositions disclosed herein comprise at least onestrain of bacteria, wherein the at least one strain of bacteriacomprises at least one protein selected from a protein that mediatesbiosynthesis of a polysaccharide, a protein that mediates biosynthesisof cell wall, a protein that mediates biosynthesis of amino acids, aprotein that mediates carbohydrate metabolism, and a protein thatmediates glycerol transportation. In some embodiments, compositionsdisclosed herein comprise at least one strain of bacteria, wherein theat least one strain of bacteria comprises at least one nucleic acid thatencodes a protein, wherein the protein mediates biosynthesis of apolysaccharide, a protein that mediates biosynthesis of cell wall, aprotein that mediates biosynthesis of amino acids, a protein thatmediates carbohydrate metabolism, and a protein that mediates glyceroltransportation. In some embodiments, the protein that mediatesbiosynthesis of a polysaccharide is a glycosyl transferase. In someembodiments, the protein that mediates biosynthesis of cell-wall is aD-alanin-D-alanine ligase. In some embodiments, the protein thatmediates amino acid biosynthesis is a cobalamin-independent methioninesynthase. In some embodiments, the protein is a glycerol uptakefacilitator protein. In some embodiments, the protein is aprotoporphyrinogen oxidase. In some embodiments, the protoporphyrinogenoxidase is encoded by a hemY gene.

In some embodiments, compositions disclosed herein comprise at least onestrain of bacteria, wherein the at least one strain of bacteriacomprises at least one nucleic acid encoding a protein that is selectedfrom a glycosyl transferase, a D-alanin-D-alanine ligase, and acobalamin-independent methionine synthase.

In certain embodiments, the bacteria have been selected, transformed, orengineered for greater expression or activity of a protein, wherein theprotein is selected from a protein that mediates biosynthesis of apolysaccharide, a protein that mediates biosynthesis of cell wall, and aprotein that mediates biosynthesis of amino acids. In certainembodiments, the bacteria have been selected, transformed, or engineeredfor greater expression or activity of a protein selected from a glycosyltransferase, a D-alanin-D-alanine ligase, and a cobalamin-independentmethionine synthase.

In some embodiments, compositions disclosed herein comprise at least onestrain of bacteria, wherein the at least one strain of bacteria does notcomprise a Christie-Atkins-Munch-Petersen (CAMP) protein. In someembodiments, compositions disclosed herein comprise at least one strainof bacteria, wherein the at least one strain of bacteria does notcomprise a CAMP1 protein. In some embodiments, compositions disclosedherein comprise at least one strain of bacteria, wherein the at leastone strain of bacteria does not comprise a CAMP2 protein. In someembodiments, compositions disclosed herein comprise at least one strainof bacteria, wherein the at least one strain of bacteria does notcomprise a CAMP3 protein.

In some embodiments, compositions disclosed herein comprise at least onestrain of bacteria, wherein the at least one strain of bacteria does notcomprise a nucleic acid encoding a CAMP protein. In certain embodiments,the bacteria have been selected, transformed, or engineered for lessexpression or activity of a CAMP protein relative to the bacteria thatis not selected, transformed or engineered. In certain embodiments, thebacteria have been selected, transformed, or engineered for noexpression or activity of a CAMP protein. In certain embodiments, thebacteria have been mutated to remove at least a portion of a nucleicacid encoding a CAMP protein. In some embodiments, the CAMP protein isselected from CAMP1, CAMP2, and CAMP3.

In some embodiments, compositions disclosed herein comprise at least onestrain of bacteria, wherein the at least one strain of bacteria does notcomprise a sialidase. In some embodiments, compositions disclosed hereincomprise at least one strain of bacteria, wherein the at least onestrain of bacteria does not comprise a nucleic acid encoding asialidase. In certain embodiments, the bacteria have been selected,transformed, or engineered for less expression or activity of asialidase relative to the bacteria that is not selected, transformed orengineered. In certain embodiments, the bacteria have been selected,transformed, or engineered for no expression or activity of a sialidase.In certain embodiments, the bacteria have been mutated to remove atleast a portion of a nucleic acid encoding a sialidase.

In some embodiments, compositions disclosed herein comprise at least onestrain of bacteria, wherein the at least one strain of bacteria does notcomprise a neuramidase. In some embodiments, compositions disclosedherein comprise at least one strain of bacteria, wherein the at leastone strain of bacteria does not comprise a nucleic acid encoding aneuramidase. In certain embodiments, the bacteria have been selected,transformed, or engineered for less expression or activity of aneuramidase relative to the bacteria that is not selected, transformedor engineered. In certain embodiments, the bacteria have been selected,transformed, or engineered for no expression or activity of aneuramidase. In certain embodiments, the bacteria have been mutated toremove at least a portion of a nucleic acid encoding a neuramidase.

In certain embodiments, the bacteria has been selected, transformed, orengineered for higher activity or expression of any of the followingproteins: Adhesion (NCBI Accession No. 50842581); CAMP factor (NCBIAccession No. 50842175, 50842711, 50842820, 50843546);Endoglycoceramidase (NCBI Accession No. 50842131); Iron transportlipoprotein (NCBI Accession No. 50841911); Lysozyme M1 (NCBI AccessionNo. 50843125); Protein PAGK_237 (NCBI Accession No. 482891444); ProteinPPA0532 (NCBI Accession No. 50842016); Protein PPA0533 (NCBI AccessionNo. 50842017); or Protein PPA1498 (NCBI Accession No. 50842976). Incertain embodiments, the bacteria has been selected, transformed, orengineered with a nucleic acid encoding any of the following protein anyof the following proteins: Adhesion (NCBI Accession No. 50842581); CAMPfactor (NCBI Accession No. 50842175, 50842711, 50842820, 50843546);Endoglycoceramidase (NCBI Accession No. 50842131); Iron transportlipoprotein (NCBI Accession No. 50841911); Lysozyme M1 (NCBI AccessionNo. 50843125); Protein PAGK_237 (NCBI Accession No. 482891444); ProteinPPA0532 (NCBI Accession No. 50842016); Protein PPA0533 (NCBI AccessionNo. 50842017); or Protein PPA1498 (NCBI Accession No. 50842976).

In certain embodiments, the bacteria has been selected, transformed, orengineered for lower activity or expression of any of the followingproteins: Adhesion (NCBI Accession No. 50843565 or 50843645); Cell wallhydrolase (NCBI Accession No. 50843410); Lipase/acylhydrolase (NCBIAccession No. 50843480); NPL/P60 protein (NCBI Accession No. 50842209);Peptide ABC transporter (NCBI Accession No. 50843590); Protein PPA1197(NCBI Accession No. 50842677); Protein PPA1281 (NCBI Accession No.50842762); Protein PPA1715 (NCBI Accession No. 50843175); ProteinPPA1939 (NCBI Accession No. 50843388); Protein PPA2239 (NCBI AccessionNo. 50843674); Rare lipoprotein A rlpa (NCBI Accession No. 50843612); orTriacylglycerol lipase (NCBI Accession No. 50843543). In certainembodiments, the bacteria has been selected, transformed, or engineeredwith a nucleotide to delete or disrupt a gene encoding any of thefollowing proteins: Adhesion (NCBI Accession No. 50843565 or 50843645);Cell wall hydrolase (NCBI Accession No. 50843410); Lipase/acylhydrolase(NCBI Accession No. 50843480); NPL/P60 protein (NCBI Accession No.50842209); Peptide ABC transporter (NCBI Accession No. 50843590);Protein PPA1197 (NCBI Accession No. 50842677); Protein PPA1281 (NCBIAccession No. 50842762); Protein PPA1715 (NCBI Accession No. 50843175);Protein PPA1939 (NCBI Accession No. 50843388); Protein PPA2239 (NCBIAccession No. 50843674); Rare lipoprotein A rlpa (NCBI Accession No.50843612); or Triacylglycerol lipase (NCBI Accession No. 50843543).

In certain embodiments, bacteria disclosed herein have been selected,transformed, or engineered for lower activity or expression of any ofthe following proteins: HMPREF0675_4855; HMPREF0675_4856;HMPREF0675_4479; HMPREF0675_4480; HMPREF0675_4481; HMPREF0675_3655/3657;HMPREF0675_4816; HMPREF0675_4817; HMPREF0675_5205; HMPREF0675_5206;HMPREF0675_5014; HMPREF0675_5101; HMPREF0675_5159; HMPREF0675_4093/4094;HMPREF0675_4163; HMPREF0675_5031; HMPREF0675_5390; HMPREF0675_3037. Incertain embodiments, the bacteria have been selected, transformed, orengineered with a nucleotide to delete or disrupt a gene encoding any ofthe following proteins: HMPREF0675_4855; HMPREF0675_4856;HMPREF0675_4479; HMPREF0675_4480; HMPREF0675_4481; HMPREF0675_3655/3657;HMPREF0675_4816; HMPREF0675_4817; HMPREF0675_5205; HMPREF0675_5206;HMPREF0675_5014; HMPREF0675_5101; HMPREF0675_5159; HMPREF0675_4093/4094;HMPREF0675_4163; HMPREF0675_5031; HMPREF0675_5390; HMPREF0675_3037.

In certain embodiments, the bacteria have been selected, transformed, orengineered for higher activity or expression of any of the followingproteins HMPREF0675_4855; HMPREF0675_4856; HMPREF0675_4479;HMPREF0675_4480; HMPREF0675_4481; HMPREF0675_3655/3657; HMPREF0675_4816;HMPREF0675_4817; HMPREF0675_5205; HMPREF0675_5206; HMPREF0675_5014;HMPREF0675_5101; HMPREF0675_5159; HMPREF0675_4093/4094; HMPREF0675_4163;HMPREF0675_5031; HMPREF0675_5390; HMPREF0675_3037. In certainembodiments, the bacteria has been selected, transformed, or engineeredwith a nucleic acid encoding any of the following proteins:HMPREF0675_4855; HMPREF0675_4856; HMPREF0675_4479; HMPREF0675_4480;HMPREF0675_4481; HMPREF0675_3655/3657; HMPREF0675_4816; HMPREF0675_4817;HMPREF0675_5205; HMPREF0675_5206; HMPREF0675_5014; HMPREF0675_5101;HMPREF0675_5159; HMPREF0675_4093/4094; HMPREF0675_4163; HMPREF0675_5031;HMPREF0675_5390; HMPREF0675_3037.

In certain embodiments, the selected, transformed, or engineeredbacteria do not comprise an antibiotic resistance gene. In certainembodiments, the selected, transformed, or engineered bacteria lack anantibiotic resistance gene to any one or more of aminoglycoside,beta-lactam, colistin, fluoroquinolone, fosfomycin, fusidic acid,macrolide, lincosamide, streptogramin B, nitroimidazole, oxazolidinone,phenicol, rifampicin, sulphonamide, tetracycline, trimethoprim, orglycopeptide. In certain embodiments, an antibiotic can be applied tohalt treatment with selected, transformed, or engineered bacteriadisclosed herein. In certain embodiments, the antibiotic isaminoglycoside, beta-lactam, colistin, fluoroquinolone, fosfomycin,fusidic acid, macrolide, lincosamide, streptogramin B, nitroimidazole,oxazolidinone, phenicol, rifampicin, sulphonamide, tetracycline,trimethoprim, or glycopeptide.

In certain embodiments, the bacteria are selected, transformed, orengineered in order to reduce expression or release of pro-inflammatorymediators by human cells of which the bacteria contact. Bacteria mayeither directly or indirectly contact human cells (e.g., human skincells). For instance, bacteria may indirectly contact human cells viafactors secreted or released from the bacteria. Non-limiting example ofpro-inflammatory mediators from human cells are IL-8, IL-1, IL-6,TNF-alpha, INF-alpha, and human beta defensin.

Mixtures of Different Microbes

Provided herein are compositions of a plurality of health-associatedmicrobes. The composition of health-associated microbes may be a mixtureof a plurality of different health-associated microbes. In a certainembodiment, the mixture comprises at least one selected, transformed, orengineered bacteria. In a certain embodiment, the mixture comprises atleast one selected, transformed, or engineered P. acnes. In certainembodiments, the mixture comprises 2, 3, 4, 5, 6, 7, 8, 9, 10 or moreisolated and purified species, strains, ribotypes, or phylotypes ofbacteria. In a certain embodiment, the mixture comprises at least onestrain of bacteria that normally colonizes a tissue or body area otherthan the skin. In a certain embodiment, the mixture comprises at leastone strain of bacteria that normally colonizes the oral cavity. Incertain embodiments, the at least one bacteria that normally colonizesthe oral cavity is S. salivarius. In a certain embodiment, the mixturecomprises at least one strain of bacteria that normally colonizes thelumen of the gastrointestinal system. In a certain embodiment, themixture comprises at least one bacteria that normally colonizes thelumen of the gastrointestinal system is a Lactobacillus or aBifidobacterium. In certain embodiments, the Bifidobacterium isBidifobacterium lactis Bb-12, Bifidobacterium animalis, Bifidobacteriumbreve, Bifidobacterium bifidum, or any combination thereof. In certainembodiments, the Lactobacillus is Lactobacillus acidophilus,Lactobacillus bulgaricus, Lactobacillus rhamnosus GG, Lactobacillusfermentumi, Lactobacillus Sakei, Lactobacillus casei, Lactobacillussalivarius, L rhamnosus LC705, Lactobacillus F19 L, Lactobacillusacidophilus La-5, or any combination thereof. In a certain embodiment,the mixture comprises at least 2, 3, 4, 5, 6, 7, 8, 9, 10, or moredifferent bacterial species. In a certain embodiment, the mixturecomprises a mixture of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, or moredifferent bacterial strains. In a certain embodiment, the mixturecontains at least one non-bacterial microbe such as a fungus, virus, orbacteriophage. Any defined mixture of a plurality of probiotic strainsmay be recited to “consist essentially of” This means that the mixtureincludes only the specified strains plus any non-active ingredientnecessary for proper administration as a topical or oral formulation,such as an excipient or diluent.

In some embodiments, compositions disclosed herein comprisehealth-associated-microbes and probiotics especially useful for treatingeczema. In some embodiments, compositions for treating eczema disclosedherein comprise Staphylococcus Aureus. In some embodiments, compositionsfor treating eczema disclosed herein comprise dead Staphylococcus Aureusbacteria. In some embodiments, compositions for treating eczemadisclosed herein comprise Staphylococcus hominis. In other embodiments,the probiotic comprises of one more of a Dermacoccus, Methlyobacteriumor Propionibacterium as they have a negative correlation with S. aureus.In other embodiments, a topical probiotic composition of S. mitis, S.sanguinis or S. cristatus are included in the probiotic.

Formulations

Provided herein, in some aspects, are compositions that comprise atleast one probiotic or health-associated microbe disclosed herein,wherein the compositions are formulated for administration to a subjectin need thereof. Generally, the subject is a human afflicted with acne,eczema, psoriasis, seborrheic dermatitis, rosacea, or any combinationthereof. In some embodiments, a composition is formulated for topicaladministration to a subject in need thereof. In some embodiments, thecompositions are formulated for topical administration to the skin ofthe subject. In some embodiments, the compositions are formulated fortopical administration to the scalp of the subject. In some embodiments,a composition is formulated for oral administration. By way ofnon-limiting example, compositions disclosed herein comprising strainsof Lactobacillus may be preferentially administered by oraladministration. In some embodiments, a composition is formulated fortransdermal administration. In some embodiments, a composition isformulated for injectable administration. In certain embodiments, thecomposition is a formulation selected from a gel, ointment, lotion,emulsion, paste, cream, foam, mousse, liquid, spray, suspension,dispersion and aerosol. In certain embodiments, the formulationcomprises one or more excipients to provide a desired form and a desiredviscosity, flow or other physical or chemical characteristic foreffective application, coverage and adhesion to skin.

Compositions disclosed herein may be presented in a formulation thatincludes one or more excipients to improve any one or more ofshelf-life, application, skin penetration, and therapeutic effect. Insome embodiments, the excipient is necessary to improve any one or moreof shelf-life, application, skin penetration, and therapeutic effect.

In certain embodiments, the health-associated microbe or probioticcompositions described herein are formulated for oral ingestion. Theoral ingestion form may be a pill, tablet, capsule, paste, liquidsuspension, colloid, or mixed with various foods such as candies, chews,yogurt, milk, cottage cheese or non-dairy based or lactose reducedsubstitutes. The formulation may contain additional non-activeingredients that improve flavor, smell, or texture of the ediblecomposition. The formulation may also include binding agents,encapsulating films, or excipients that preserve shelf-life andbioavailability.

In certain embodiments, health-associated-microbes and probioticcompositions disclosed herein that are administered orally comprise aspecies of bacteria selected from L. acidophilus La-5, Bifidobacteriumanimalis, Lactobacillus rhamnosus, Lactobacillus F19, Lactobacillusfermentum, Lactobacillus Sakei, Lactobacillus reuteri, Bifidobacteriumbreve, Propionibacterium freudenreichii ssp. Shermanii JS,Bifidobacterium bifidum, Lactobacillus acidophilus, Lactobacillus casei,and Lactobacillus salivarius, and combinations thereof. In someembodiments, the composition comprises Lactobacillus salivarius and afructo-oligosaccharide. In some embodiments, the composition comprisesLactobacillus rhamnosus GG. In some embodiments, the compositioncomprises Lactobacillus rhamnosus LC705. In some embodiments, thecomposition comprises Lactobacillus salivarius and a prebiotic. In someembodiments, the composition comprises hydrolyzed whey formula withLactobacillus rhamnosus GG. In some embodiments, the compositioncomprises hydrolyzed whey formula with Bifidobacterium lactis Bb-12. Incertain embodiments, health-associated-microbes and probioticcompositions disclosed herein that are administered orally comprisebacteria selected from Lactobacillus rhamnosus GG and bifidobacteriaBb-12, and a combination thereof.

An emulsion may be described as a preparation of one liquid distributedin small globules throughout the body of a second liquid. In someembodiments, the dispersed liquid is the discontinuous phase, and thedispersion medium is the continuous phase. When oil is the dispersedliquid and an aqueous solution is the continuous phase, it is known asan oil-in-water emulsion, whereas when water or aqueous solution is thedispersed phase and oil or oleaginous substance is the continuous phase,it is known as a water-in-oil emulsion. The oil phase may consist atleast in part of a propellant, such as an HFA propellant. Either or bothof the oil phase and the aqueous phase may contain one or moresurfactants, emulsifiers, emulsion stabilizers, buffers, and otherexcipients. Preferred excipients include surfactants, especiallynon-ionic surfactants; emulsifying agents, especially emulsifying waxes;and liquid non-volatile non-aqueous materials, particularly glycols suchas propylene glycol. The oil phase may contain other oilypharmaceutically approved excipients. For example, materials such ashydroxylated castor oil or sesame oil may be used in the oil phase assurfactants or emulsifiers.

A lotion may be described as a low- to medium-viscosity liquidformulation. A lotion can contain finely powdered substances that are insoluble in the dispersion medium through the use of suspending agentsand dispersing agents. Alternatively, lotions can have as the dispersedphase liquid substances that are immiscible with the vehicle and areusually dispersed by means of emulsifying agents or other suitablestabilizers. In one embodiment, the lotion is in the form of an emulsionhaving a viscosity of between 100 and 1000 centistokes. The fluidity oflotions permits rapid and uniform application over a wide surface area.Lotions are typically intended to dry on the skin leaving a thin coat oftheir medicinal components on the skin's surface.

A cream may be described as a viscous liquid or semi-solid emulsion ofeither the “oil-in-water” or “water-in-oil type”. Creams may containemulsifying agents and/or other stabilizing agents. In one embodiment,the formulation is in the form of a cream having a viscosity of greaterthan 1000 centistokes, typically in the range of 20,000-50,000centistokes. Creams are often time preferred over ointments as they aregenerally easier to spread and easier to remove.

The basic difference between a cream and a lotion is the viscosity,which is dependent on the amount/use of various oils and the percentageof water used to prepare the formulations. Creams are typically thickerthan lotions, may have various uses and often one uses more variedoils/butters, depending upon the desired effect upon the skin. In acream formulation, the water-base percentage is about 60-75% and theoil-base is about 20-30% of the total, with the other percentages beingthe emulsifier agent, preservatives and additives for a total of 100%.

An ointment may be described as a semisolid preparation containing anointment base and optionally one or more active agents of thisdisclosure. Examples of suitable ointment bases include hydrocarbonbases (e.g., petrolatum, white petrolatum, yellow ointment, and mineraloil); absorption bases (hydrophilic petrolatum, anhydrous lanolin,lanolin, and cold cream); water-removable bases (e.g., hydrophilicointment), and water-soluble bases (e.g., polyethylene glycolointments). Pastes typically differ from ointments in that they containa larger percentage of solids. Pastes are typically more absorptive andless greasy that ointments prepared with the same components.

A gel may be described as a semisolid system containing dispersions ofsmall or large molecules in a liquid vehicle that is rendered semisolidby the action of a thickening agent or polymeric material dissolved orsuspended in the liquid vehicle. The liquid may include a lipophiliccomponent, an aqueous component or both. Some emulsions may be gels orotherwise include a gel component. Some gels, however, are not emulsionsbecause they do not contain a homogenized blend of immisciblecomponents. Suitable gelling agents include, but are not limited to,modified celluloses, such as hydroxypropyl cellulose and hydroxyethylcellulose; Carbopol homopolymers and copolymers; and combinationsthereof. Suitable solvents in the liquid vehicle include, but are notlimited to, diglycol monoethyl ether; alkene glycols, such as propyleneglycol; dimethyl isosorbide; alcohols, such as isopropyl alcohol andethanol. The solvents are typically selected for their ability todissolve the drug. Other additives, which improve the skin feel and/oremolliency of the formulation, may also be incorporated. Examples ofsuch additives include, but are not limited, isopropyl myristate, ethylacetate, C12-C15 alkyl benzoates, mineral oil, squalane, cyclomethicone,capric/caprylic triglycerides, and combinations thereof.

Foams may be described as an emulsion in combination with a gaseouspropellant. The gaseous propellant consists primarily ofhydrofluoroalkanes (HFAs). Suitable propellants include HFAs such as1,1,1,2-tetrafluoroethane (HFA 134a) and1,1,1,2,3,3,3-heptafluoropropane (HFA 227), but mixtures and admixturesof these and other HFAs that are currently approved or may becomeapproved for medical use are suitable. The propellants preferably arenot hydrocarbon propellant gases which can produce flammable orexplosive vapors during spraying. Furthermore, the compositionspreferably contain no volatile alcohols, which can produce flammable orexplosive vapors during use.

Emollients may be described as externally applied agents that soften orsoothe skin and are generally known in the art and listed in compendia,such as the “Handbook of Pharmaceutical Excipients”, 4.sup.th Ed.,Pharmaceutical Press, 2003. In certain embodiments, the emollients arealmond oil, castor oil, ceratonia extract, cetostearoyl alcohol, cetylalcohol, cetyl esters wax, cholesterol, cottonseed oil, cyclomethicone,ethylene glycol palmitostearate, glycerin, glycerin monostearate,glyceryl monooleate, isopropyl myristate, isopropyl palmitate, lanolin,lecithin, light mineral oil, medium-chain triglycerides, mineral oil andlanolin alcohols, petrolatum, petrolatum and lanolin alcohols, soybeanoil, starch, stearyl alcohol, sunflower oil, xylitol and combinationsthereof. In one embodiment, the emollients are ethylhexylstearate andethylhexyl palmitate.

Surfactants are surface-active agents that lower surface tension andthereby increase the emulsifying, foaming, dispersing, spreading andwetting properties of a product. In certain embodiments, suitablenon-ionic surfactants include emulsifying wax, glyceryl monooleate,polyoxyethylene alkyl ethers, polyoxyethylene castor oil derivatives,polysorbate, sorbitan esters, benzyl alcohol, benzyl benzoate,cyclodextrins, glycerin monostearate, poloxamer, povidone andcombinations thereof. In one embodiment, the non-ionic surfactant isstearyl alcohol.

Emulsifiers are surface active substances which promote the suspensionof one liquid in another and promote the formation of a stable mixture,or emulsion, of oil and water. In certain embodiments, the emulsifiersare metallic soaps, certain animal and vegetable oils, and various polarcompounds. Suitable emulsifiers include acacia, anionic emulsifying wax,calcium stearate, carbomers, cetostearyl alcohol, cetyl alcohol,cholesterol, diethanolamine, ethylene glycol palmitostearate, glycerinmonostearate, glyceryl monooleate, hydroxpropyl cellulose, hypromellose,lanolin, hydrous, lanolin alcohols, lecithin, medium-chaintriglycerides, methylcellulose, mineral oil and lanolin alcohols,monobasic sodium phosphate, monoethanolamine, nonionic emulsifying wax,oleic acid, poloxamer, poloxamers, polyoxyethylene alkyl ethers,polyoxyethylene castor oil derivatives, polyoxyethylene sorbitan fattyacid esters, polyoxyethylene stearates, propylene glycol alginate,self-emulsifying glyceryl monostearate, sodium citrate dehydrate, sodiumlauryl sulfate, sorbitan esters, stearic acid, sunflower oil,tragacanth, triethanolamine, xanthan gum and combinations thereof. Inone embodiment, the emulsifier is glycerol stearate. In one embodiment,the emulsifier is glycerol. In one embodiment, the emulsifier isglycerin.

In some embodiments, compositions disclosed herein are formulated to beapplied to a subject's scalp. In some embodiments, the composition isformulated to be used as a product selected from a shampoo, aconditioner, a mousse, a gel, and a spray. Such compositions would beuseful for the treatment of seborrheic dermatitis. Treatment ofseborrheic dermatitis with such compositions may result in the reductionof a symptom selected from dandruff and cradle cap. However,compositions disclosed herein may be used to treat seborrheic dermatitisat other areas of the body besides the scalp. Non-limiting examples ofother areas include the chest, stomach, skin folds, arms, legs, groinarea and under breasts.

In some embodiments, compositions disclosed herein comprise a buffer,wherein the buffer controls a pH of the composition. Preferably, thebuffers buffer the composition from a pH of about 4 to a pH of about7.5, from a pH of about 4 to a pH of about 7, and from a pH of about 5to a pH of about 7.

In some embodiments, compositions disclosed herein are formulated toprovide or maintain a desirable skin pH. In some embodiments, thedesirable skin pH is between about 4.5 and about 6.5. In someembodiments, the desirable skin pH is between about 5 and about 6. Insome embodiments, the desirable skin pH is about 5.5. In someembodiments, compositions disclosed herein are formulated with a skin pHmodulating agent. Non-limiting examples of pH modulating agents includesalicylic acid, glycolic acid, trichloroacetic acid, azeilic acid,lactic acid, aspartic acid, hydrochloride, stearic acid, glycerylstearate, cetyl palmitate, urea phosphate, and tocopheryl acetate.

In some embodiments, compositions disclosed herein are formulated toprovide more oxygen to the skin. In some embodiments, compositionsdisclosed herein are formulated to provide more oxygen exposure to theskin. In some embodiments, compositions disclosed herein are formulatedto provide more oxygen diffusion into the skin. In some embodiments,compositions disclosed herein are formulated to provide more oxygendiffusion through the skin. In some embodiments, compositions disclosedherein are formulated with an agent that provides more oxygen to theskin. In some embodiments, compositions disclosed herein are used withan agent that provides more oxygen to the skin. In some embodiments,compositions disclosed herein are used before use of an agent thatprovides more oxygen to the skin. In some embodiments, compositionsdisclosed herein are used after use of an agent that provides moreoxygen to the skin. A non-limiting example of an agent that providesoxygen to the skin is chlorophyll.

Preservatives can be used to prevent the growth of fungi andmicroorganisms. Suitable antifungal and antimicrobial agents include,but are not limited to, benzoic acid, butylparaben, ethyl paraben,methyl paraben, propylparaben, sodium benzoate, sodium propionate,benzalkonium chloride, benzethonium chloride, benzyl alcohol,cetylpyridinium chloride, chlorobutanol, phenol, phenylethyl alcohol,and thimerosal. In one embodiment, a concentration of a preservativethat is effective to prevent fungal growth is selected, withoutaffecting the effectiveness of the composition for its intended purposedupon topical application.

Excipients in the formulation are selected based on the type offormulation intended. In certain embodiments, the excipients includegelatin, casein, lecithin, gum acacia, cholesterol, tragacanth, stearicacid, benzalkonium chloride, calcium stearate, glyceryl monostearate,cetostearyl alcohol, cetomacrogol emulsifying wax, sorbitan esters,polyoxyethylene alkyl ethers, polyoxyethylene castor oil derivatives,polyoxyethylene sorbitan fatty acid esters, polyethylene glycols,polyoxyethylene stearates, colloidol silicon dioxide, phosphates, sodiumdodecyl sulfate, carboxymethylcellulose calcium, carboxymethylcellulosesodium, methylcellulose, hydroxyethylcellulose, hydroxypropylcellulose,hydroxypropylmethycellulose phthalate, noncrystalline cellulose,magnesium aluminum silicate, triethanolamine, polyvinyl alcohol,polyvinylpyrrolidone, sugars, and starches.

In some embodiments, compositions disclosed herein are formulated withglycerol. In some instances, a strain of bacteria in the compositionferments the glycerol, thereby producing short chain fatty acids.Non-limiting examples of short-chain fatty acids include acetic acid,lactic acid, and propionic acid. In some embodiments, the strain ofbacteria is a Propionibacterium strain. In some embodiments, the strainof bacteria is a P. acnes strain.

Penetration enhancers are frequently used to promote transdermaldelivery of drugs across the skin, in particular across the stratumcorneum. Some penetration enhancers cause dermal irritation, dermaltoxicity and dermal allergies. However, the more commonly used onesinclude urea, (carbonyldiamide), imidurea, N,N-diethylformamide,N-methyl-2-pyrrolidine, 1-dodecal-azacyclopheptane-2-one, calciumthioglycate, 2-pyyrolidine, N,N-diethyl-m-toluamide, oleic acid and itsester derivatives, such as methyl, ethyl, propyl, isopropyl, butyl,vinyl and glycerylmonooleate, sorbitan esters, such as sorbitanmonolaurate and sorbitan monooleate, other fatty acid esters such asisopropyl laurate, isopropyl myristate, isopropyl palmitate, diisopropyladipate, propylene glycol monolaurate, propylene glycol monooleatea andnon-ionic detergents such as BRIJ® 76 (stearyl poly(10) oxyethyleneether), BRIJ® 78 (stearyl poly(20)oxyethylene ether), BRIJ® 96 (oleylpoly(10)oxyethylene ether), and BRIJ® 721 (stearyl poly (21) oxyethyleneether) (ICI Americas Inc. Corp.).

The composition can be formulated to comprise the health-associatedmicrobe or probiotic at a particular concentration. For example, thecomposition can comprise an amount of probiotic such that themicroorganisms may be delivered in effective amounts. In certainembodiments, the amount of probiotic delivered is at least 1×10³, 1×10⁴,1×10⁵, 1×10⁶, 1×10⁷, 1×10⁸, 1×10⁹, 1×10¹⁰ colony forming units per unitdose. The composition may be formulated with the health-associatedmicrobe or probiotic in a proportion of at least about 0.0001%(expressed by dry weight), from about 0.0001% to about 99%, from about0.001% to about 90% by weight, from about 0.01% to about 80% by weight,and from about 0.1% to about 70% by weight, relative to the total weightof the composition. In general, a composition intended to beadministered topically comprises at least 1×10³, 1×10⁴, 1×10⁵, 1×10⁶,1×10⁷, 1×10⁸, 1×10⁹, 1×10¹⁰ microorganisms per gram of carrier, or atequivalent doses calculated for inactive or dead microorganisms or forbacterial fractions or for metabolites produced.

Microbes disclosed herein may be delivered in effective amounts per unitdose, of at least about 1×10² colony forming units (cfu) to about 1×10²⁰cfu. In the particular case of the compositions that have to beadministered topically, the concentration of each bacterial strainand/or corresponding fraction and/or metabolite can be adjusted so as tocorrespond to doses (expressed as bacterial equivalent) ranging fromabout 1×10⁵ to about 1×10¹² cfu/dose.

Compositions disclosed herein for topical application generally comprisefrom about 1×10² to about 1×10¹⁵ cfu/g, from about 1×10⁵ to about 1×10¹²cfu/g, or from about 1×10⁶ to about 10×10¹² cfu/g of bacteria.

In certain embodiments, compositions disclosed herein are formulated inorder to deliver at least 10⁶ microbes per cm² of skin. In certainembodiments, the composition is formulated in order to deliver at least10⁷ microbes per cm² of skin. In certain embodiments, the composition isformulated in order to deliver at least 10⁸ microbes per cm² of skin. Incertain embodiments, the composition is formulated in order to deliverat least 10⁹ microbes per cm² of skin. In certain embodiments, thecomposition is formulated in order to deliver less than 10⁹ microbes percm² of skin. In certain embodiments, the composition is formulated inorder to deliver less than 10⁸ microbes per cm² of skin. In certainembodiments, the composition is formulated in order to deliver less than10⁷ microbes per cm² of skin. In certain embodiments, the composition isformulated in order to deliver between about 10⁷ and 10⁸ microbes percm² of skin. In certain embodiments, the composition is formulated inorder to deliver between about 10⁶ microbes per cm² of skin and about10¹⁰ microbes per cm² of skin. In certain embodiments, the compositionis formulated in order to deliver between about 10⁶ microbes per cm² ofskin and about 10⁹ microbes per cm² of skin. In certain embodiments, thecomposition is formulated in order to deliver between about 10⁷ microbesper cm² of skin and about 10¹⁰ microbes per cm² of skin. In certainembodiments, the composition is formulated in order to deliver betweenabout 10⁷ microbes per cm² of skin and about 10⁹ microbes per cm² ofskin.

In certain embodiments, compositions disclosed herein are formulated ata concentration of about 10⁵ microbes per milliliter to about 10¹²microbes per milliliter. In certain embodiments, compositions disclosedherein are formulated at a concentration of about 10⁶ microbes permilliliter. In certain embodiments, compositions disclosed herein areformulated at a concentration of about 10⁷ microbes per milliliter. Incertain embodiments, compositions disclosed herein are formulated at aconcentration of about 10⁸ microbes per milliliter. In certainembodiments, compositions disclosed herein are formulated at aconcentration of about 10⁹ microbes per milliliter. In certainembodiments, compositions disclosed herein are formulated at aconcentration of about 10¹⁰ microbes per milliliter.

In certain embodiments, compositions disclosed herein for topical ororal use contain biologic stability compounds including but not limitedto carbohydrates such as trehalose, mannose, fructose, glucose, sucrose,lactose, raffinose, stachyose, melezitose, dextran, and sugar alcohols;and/or cryopreservatives such as glycerol, bovine-free media, (e.g.,tryptic soy broth), whey protein, NaCl, phosphate buffer, MgCl,lyophilized bacteria, or other inactive/killed bacteria.

After formulation, composition disclosed herein may be packaged in amanner suitable for delivery and use by an end user. In one embodiment,the composition is placed into an appropriate dispenser and shipped tothe end user. Examples of a final container may include a pump bottle,squeeze bottle, jar, tube, capsule or vial.

In some embodiments, compositions disclosed herein can be added to anapplicator before packaging. Non-limiting examples of applicatorsinclude a cotton pad, a polyester pad, a q-tip, a sponge, and a brush.In some embodiments, the applicator is placed in a package. Non-limitingexamples of a package includes bags and foil or wax lined paper packets.The interior of the package may be sterile. In some embodiments, air inthe package is removed with a vacuum before sealing. In someembodiments, the package is heat-sealed. In some embodiments, thepackage is sealed with adhesive.

In another embodiment, compositions disclosed herein are lyophilized orfreeze dried, for reconstitution before application to the skin. In oneembodiment, lyophilization or freeze drying is conducted with one ormore excipients, such as glycerol or other sugar alcohols, to improvethe shelf life of the selected, transformed, or engineered bacteria. Inone embodiment, the lyophilized composition does not include trehalose(.alpha.-D-glucopyranosyl-1,1-.alpha.-D-glucopyranosyde). In someembodiments, the composition does not have to be frozen.

Compositions disclosed herein may be packaged in one or more containers.For example, a single bottle, tube, container, or capsule may be dividedto two equal or unequal parts wherein one part contains the bacteria, intheir packing form (freeze dried/inactive, etc.), and the other partcontains an activation material, which can be a liquid or a gel. Thesingle bottle or container can be designed so that an end user candispense with a single force applied to the container all or a portionof the contents in the two container parts, to dispense onto the skin orother surface the selected, transformed, or engineered bacteria and theactivation material. The kit may also be of the form that comprises twoor more containers, one container with the population(s) of selected,transformed, or engineered bacteria and the other with a formulation foradmixture with the populations of selected, transformed, or engineeredbacteria. In another example, two or more containers, one container withthe population of selected, transformed, or engineered bacteria, theother container with natural nonpathogenic skin bacteria that are notselected, transformed, or engineered, and a third container with aformulation for admixture with the populations of selected, transformed,or engineered bacteria. In another example, the two or more containerscomposing the single bottle had one pump connected to two separatetubes, each draining from a different chamber. The kit may also includeone or more complementary products, such as soaps, body washes ormoisturizing lotions with certain pH, lotions or creams containingactive compounds, bacteria and limiting factors etc. In anotherembodiment, the complementary product is a limiting factor that willenhance the growth, activity and/or expression of the compound ofinterest to provide a lasting or continuous expression of the compound.The complementary product may include any compound beneficial to theactivity of the original product, and enhance its activity for lastingefficacy. Another contemplated packaging is one wherein the populationof selected, transformed, or engineered bacteria is maintained as alayer on a bandage or film that is combined with a second layer ofbandage/film that will allow activation of the bacteria, and thatoptionally may also limit reproduction/growth factors. In anotherembodiment, the final product is stored refrigerated, with the bacteriabeing in their active state. In another embodiment, the bacteria arestored in a small bead of water soluble cellulose. The beads can bemixed in any solution such as sunscreen/moisturizing/body wash or soap.

In yet another embodiment, this disclosure provides for compositionscomprising a healthy skin microbiome transplant. Healthy skin microbiometransplants disclosed herein comprise a population of bacteria harvestedfrom healthy or normal skin. Healthy skin microbiome transplantsdisclosed herein can be characterized as microbiomes that induce a lowlevel of human inflammatory mediators (at the RNA and/or protein level)from a population of human cells when the microbiome is incubated withthe population of human cells. The population of human cells may be asubject's own keratinocytes. The population of human cells may be pooledkeratinocytes. Non-limiting examples of inflammatory mediators includeacne associated inflammatory markers such as IL-8, IL-6, TNF-alpha,INF-alpha, IL-1, and beta defensin. Methods of measuring levels of thesemediators either at the mRNA, protein or functional level are known inthe art and include, quantitative real-time PCR, northern blot, RNA-seq,microarray, ELISA, homogenous protein assays, immunoblot, or massspectrometry.

In yet other embodiments are compositions comprising an individual's ownmodified microbiome. Compositions comprising an individual's ownmodified microbiome may be obtained by methods disclosed herein. In someembodiments, the individual's own modified microbiome is produced byharvesting or capturing the individual's own microbiome (e.g., from askin swab), culturing the microbiome, and removing at least oneinflammatory strain of bacteria. In some embodiments, the individual'sown modified microbiome is produced by harvesting or capturing theindividual's own microbiome (e.g., from a skin swab), culturing themicrobiome, and removing at least one pathogenic strain of bacteria. Insome embodiments, an inflammatory strain is a pathogenic strain. In someembodiments, an inflammatory strain or pathogenic strain is identifiedby incubating the strain with keratinocytes and detecting production ofinflammatory mediators from the keratinocytes. In some embodiments, aninflammatory strain or pathogenic strain is identified by incubating thestrain with keratinocytes and quantifying production of inflammatorymediators from the keratinocytes (e.g., the strain produces higherlevels of inflammatory mediators from the keratinocytes than ahealth-associated strain disclosed herein). In some embodiments, aninflammatory strain or pathogenic strain is identified by incubating thestrain with keratinocytes and detecting undesirable keratinocyte geneexpression or undesirable keratinocyte activity. Undesirablekeratinocyte gene expression or undesirable keratinocyte activity wouldgenerally be understood by one skilled in the art to mean expression oractivity in keratinocytes that promotes a skin disorder. In someinstances, the keratinocytes are the subject's keratinocytes. In someinstances, the keratinocytes are pooled keratinocytes. In someinstances, methods comprise identifying and removing known acneassociated strains such as, by way of non-limiting example, some P.acnes strains of ribotypes RT4 and RT5, and clade Ia bacteria. In someinstances, methods comprise identifying and selecting onlynon-inflammatory strains identified by the method above or known to beassociated with healthy skin and introducing the modified biome to thepatient. Non-limiting examples of non-inflammatory strains include P.acnes strains of ribotypes RT2, RT6, and clade II bacteria.

In yet another embodiment is a composition comprising a microbiome froma healthy individual's stool. These compositions may be referred toherein as a “fecal transplant.” In some embodiments, the microbiome is acomplete microbiome of a healthy individual's stool. In someembodiments, the microbiome is a partial microbiome of a healthyindividual's stool. In some instances, the healthy individual does nothave acne. In some instances, the healthy individual does not have aninflammatory condition. In some instances, the healthy individual doesnot have an inflammatory skin condition. Non-limiting examples ofinflammatory conditions are acne, eczema, psoriasis, seborrheicdermatitis, rosacea, lupus, pemphigus, pemphigoid, scleroderma, alopeciaareata, lichen sclerosis, lichen planus, pruritus, prurigo nodularis,lichen simplex chronicus, inflammatory bowel disease, colitis, irritablebowel syndrome, atherosclerosis, CAD, diabetes, HIV, and cancer. In someembodiments, the healthy individual is not a tissue transplant patients,is not taking an immunosuppressive drug, or is not currently/recently(within 12 weeks) receiving an antibiotic therapy. In some embodiments,the microbiome comprises strains of bacteria that produce noinflammatory mediators when co-incubated colonic mucosal cells. In someembodiments, strains of bacteria that produce no inflammatory mediatorswhen co-incubated colonic mucosal cells are identified by 16S, 18S, orwhole genome sequencing. In some embodiments, the partial microbiome isa modified microbiome, wherein the modified microbiome is derived from afecal transplant by removing pathogenic strains or introducinghealth-associated strains.

Additional Active Ingredients

Compositions disclosed herein may comprise additional activeingredients. In certain embodiments, compositions disclosed hereincomprise at least one non-living, non-microbial constituent. By way ofnon-limiting example, the non-living, non-microbial constituent may beselected from a small molecule, a fatty acid, an antibiotic, ametabolite, an antioxidant, and a retinoid. Non-limiting examples ofantioxidants are vitamin C and vitamin E. Non-limiting examples of aretinoid are tretinoin, tazarotene, adapalene, and retinol. In someembodiments, the non-living, non-microbial constituent is vitamin D,which may be in the form of calciptotriene. In some embodiments, theadditional active ingredient is an agent that has anti-inflammatoryactivity.

In certain embodiments, the composition contains an antibiotic.Non-limiting examples of antibiotics include macrolide, tetracycline,β-lactam, aminoglycoside, cephalosporin, carbapenems,quinolone/fluoroquinolone, sulfonamides, salicylic acid, glycolic acid,azaleic acid, live phage therapy, synthetic phage contractile nanotubes,laser, dapsone, benzoyl peroxide, benzoyl peroxide/resveratrolcombinations, and any combination thereof. In some embodiments, theantibiotic is selected from clindamycin, doxycycline, erythromycin, andtetracycline, wherein the antibiotic is formulated for topicaladministration. In some embodiments, the antibiotic is selected fromerythromycin, tetracycline, doxycycline and minocycline, wherein theantibiotic is formulated for oral administration.

In certain embodiments, a composition disclosed herein comprises atopical anti-acne medication such as benzoyl peroxide or salicylic acid.The concentration of benzoyl peroxide or salicylic acid included in acomposition may be lower than that commonly included in a singleformulation (without a health-associated microbe or probiotic). In someembodiments, the concentration of the anti-acne medication is betweenabout 0.1% and about 3%. In some embodiments, the concentration of theanti-acne medication is between about 0.1% and about 2.5%. In someembodiments, the concentration of the anti-acne medication is betweenabout 0.5% and about 2.5%. In some embodiments, the concentration of theanti-acne medication is between about 1% and about 2.5%. In someembodiments, the concentration of the anti-acne medication is less thanabout 2.5%. In some embodiments, the concentration of the anti-acnemedication is less than about 2%. In some embodiments, the concentrationof the anti-acne medication is less than about 1.5%. In someembodiments, the concentration of the anti-acne medication is less thanabout 1%. In some embodiments, the concentration of the anti-acnemedication is less than about 0.5%. In some embodiments, theconcentration of the anti-acne medication is less than about 0.1%.

In certain embodiments, compositions disclosed herein comprise a topicalanti-acne medication such as a retinoid. Non-limiting examples oftopical retinoid compounds include retinoic acid, tretinoin, adapalene,and tazarotene. In certain embodiments, compositions disclosed hereincomprise resveratrol or trans-resveratrol. In some embodiments, theconcentration of the retinoid or resveratrol in the composition is lessthan about 10%. In some embodiments, the concentration of the retinoidor resveratrol in the composition is less than about 5%. In someembodiments, the concentration of the retinoid or resveratrol in thecomposition is less than about 2.5%. In some embodiments, theconcentration of the retinoid or resveratrol in the composition is lessthan about 1%. In some embodiments, the concentration of the retinoid orresveratrol in the composition is less than about 0.5%. In someembodiments, the concentration of the retinoid or resveratrol in thecomposition is between about 0.5% and about 10%. In some embodiments,the concentration of the retinoid or resveratrol in the composition isbetween about 1% and about 10%. In some embodiments, the concentrationof the retinoid or resveratrol in the composition is between about 0.5%and about 2.5%.

In some embodiments, compositions disclosed herein comprise at least oneomega-3 fatty acid. Non-limiting examples of omega-3 fatty acids includehexadecatrienoic acid (HTA), α-Linolenic acid (ALA), stearidonic acid(SDA), eicosatrienoic acid (ETE), eicosatetraenoic acid (ETA),eicosapentaenoic acid (EPA), heneicosapentaenoic acid (HPA),docosapentaenoic acid (DPA), clupanodonic acid, docosahexaenoic acid(DHA), tetracosapentaenoic acid, tetracosahexaenoic acid (nisinic acid),and phytosphingosine.

In some embodiments, compositions disclosed herein comprise an acidselected from glycolic acid, azaelic acid, and trichloroacetic acid. Insome embodiments, compositions disclosed herein comprise a naturalextract, such as tea tree oil or green tea extract.

In some embodiments, the additional active ingredient comprises a drugtargeting at least one strain of P. acnes. In some embodiments, the drugtargeting at least one strain of P. acnes is a small molecule drug. Insome embodiments, the drug targeting at least one strain of P. acnes isa small molecule inhibitor of an enzyme expressed by P. acnes. In someembodiments, the enzyme expressed by P. acnes is required for P. acnesgrowth or P. acnes energy metabolism. In some embodiments, the drugtargeting at least one strain of P. acnes is a biologic. In someembodiments, the biologic comprises a peptide. In some embodiments, thebiologic comprises an antibody or antigen binding fragment. In someembodiments, the biologic comprises and antibody-small moleculeconjugate. In some embodiments, the biologic comprises and antibody-drugconjugate. In some embodiments, the biologic comprises a nucleic acid.In some embodiments, then nucleic acid comprises an antisense nucleicacid molecule, wherein the antisense nucleic acid molecule inhibits anenzyme expressed by P. acnes. In some embodiments, the enzyme expressedby P. acnes is required for P. acnes growth or P. acnes energymetabolism. In some embodiments, the antisense nucleic acid moleculecomprises siRNA. In some embodiments, the antisense nucleic acidmolecule comprises a shRNA. In some embodiments, the antisense nucleicacid molecule comprises a guide RNA to be used with a CRISPR-associatedprotease. In some embodiments, the additional active ingredient (e.g.,guide RNA and CRISPR-associated protease) and targets a genomic elementspecific for strains of P. acnes associated with acne.

Methods of Treating Skin Disorders

Provided herein, in some aspects, are methods for treating or preventingskin disorders disclosed herein. In some aspects, the methods compriseadministering a strain of bacteria disclosed herein, wherein the strainof bacteria is incorporated into a pharmaceutical composition. In someaspects, the methods comprise administering a composition disclosedherein. In some aspects, the disclosure provides methods for treating orpreventing acne. Methods for treating or preventing acne generallycomprise administering an effective amount of a strain of bacteriadisclosed herein to the skin of a subject in need thereof. In someembodiments, methods comprise administering at least one compositiondisclosed herein. In some embodiments, methods comprise administering atleast one species of bacteria disclosed herein. In some embodiments,methods comprise administering at least one strain of bacteria disclosedherein. In some embodiments, methods comprise administering at least oneribotype of bacteria disclosed herein. In some embodiments, methodscomprise administering at least one probiotic disclosed herein. In someembodiments, methods comprise administering at least onehealth-associated microbe disclosed herein. In some embodiments, methodscomprise administering at least one selected species of selectedbacteria disclosed herein. In some embodiments, methods compriseadministering at least one selected strain of selected bacteriadisclosed herein. In some embodiments, methods comprise administering atleast one selected, transformed, or engineered bacteria disclosedherein. In some embodiments, methods comprise administering at least onegenetically modified bacteria disclosed herein. In some embodiments,methods comprise administering at least one genetically engineeredbacteria disclosed herein. In some embodiments, methods compriseadministering at least one health-associated strain of bacteriadescribed herein.

In some embodiments, methods disclosed herein comprise administering anisolated strain of bacteria. In some embodiments, methods disclosedherein comprise administering an isolated strain of bacteria. In someembodiments, methods disclosed herein comprise administering a purifiedstrain of bacteria. In some embodiments, methods disclosed hereincomprise administering a purified and isolated strain of bacteria. Insome embodiments, methods disclosed herein comprise selecting,isolating, or purifying a strain of bacteria. Selecting, isolating orpurifying may comprise isolating a single clone of bacteria andpropagating it to obtain a selected, isolated, or purified strain. Insome embodiments, the methods comprise selecting, isolating or purifyinga plurality of strains of bacteria to obtain at least a first selected,isolated, or purified strain and a second selected, isolated, orpurified strain. In some embodiments, the methods further comprisecombining the first selected, isolated, or purified strain and thesecond selected, isolated, or purified strain in a pharmaceuticalcomposition. In some embodiments, the first selected, isolated, orpurified strain or the second selected, isolated, or purified strain isselected from strains disclosed herein.

In some embodiments, the first selected, isolated, or purified strainand the second selected, isolated, or purified strain are selected fromstrains disclosed herein.

In some embodiments, methods comprise administering at least onehealth-associated strain of bacteria selected from a health-associatedstrain of Propionibacterium, Staphylococcus and Lactobacillus bacteria.In some embodiments, methods comprise administering at least onehealth-associated strain of Propionibacterium bacteria. In someembodiments, methods comprise administering at least onehealth-associated strain selected from a health-associated strain of P.acnes, a health-associated strain of P. granulosum, a health-associatedstrain of P. avidum, a health-associated strain of P. acnes subsp.defendens, and a health-associated Staphylococcus, as described herein.In some embodiments, the health-associated strain of P. acnes is not P.acnes subsp. acnes. In some embodiments, methods comprise administeringat least one health-associated strain of P. acnes. In some embodiments,methods comprise administering at least one health-associated fungus.The health-associated fungus may be Malassezia.

In some embodiments, the methods comprise administering a microbedisclosed herein. In some embodiments, the methods compriseadministering a mixture of at least two microbes disclosed herein. Insome embodiments, the methods comprise administering at least onehealth-associated microbe disclosed herein. In some embodiments, themicrobe is a fungus. In some embodiments, the microbe is a protist. Insome embodiments, the microbe is bacteria. In some embodiments, thebacteria comprise a strain of Propionibacterium bacteria. In someembodiments, the bacteria comprise a strain of P. acnes. In someembodiments, the bacteria comprise a strain of P. avidum. In someembodiments, the bacteria comprise a strain of P. granulosum. In someembodiments, the bacteria comprise a strain of P. acnes subsp.defendens. In some embodiments, the bacteria consist essentially of atleast one strain of P. acnes. In some embodiments, the bacteria consistessentially of at least one strain of P. avidum. In some embodiments,the bacteria consist essentially of at least one strain of P.granulosum. In some embodiments, the bacteria consist essentially of atleast one strain of P. acnes subsp. defendens.

In some embodiments, methods comprise administering a compositiondisclosed herein. In some embodiments, methods comprise administering acomposition having a formulation disclosed herein.

In certain embodiments, methods disclosed herein comprise applying aneffective amount of a composition containing a plurality of microbes ofdifferent ribotypes. In certain embodiments, the strain is a P. acnesstrain of a ribotype selected from RT1, RT2, RT3, RT4, RT5, RT7, RT8,RT9, and RT10. In certain embodiments, the strain is a P. acnes strainof a ribotype selected from RT1, RT2, RT3, RT7, RT8, RT9, and RT10. Incertain embodiments, the plurality of microbes is a mixture of two ormore P. acnes strains of different ribotypes. In certain embodiments,the different ribotypes comprise RT1 and RT2. In certain embodiments,the different ribotypes comprises RT1 and RT3. In certain embodiments,the different ribotypes comprise RT1 and not RT6. In certainembodiments, the different ribotypes comprise RT2 and RT3. In certainembodiments, the v comprises RT2 and not RT6. In certain embodiments,the different ribotypes comprise RT2 and RT3. In certain embodiments,the different ribotypes comprise RT3 and not RT6. In certainembodiments, the different ribotypes consist essentially of RT1 and RT2.In certain embodiments, the different ribotypes consist essentially ofRT1 and RT3. In certain embodiments, the different ribotypes consistessentially of RT1 and not RT6. In certain embodiments, the differentribotypes consist essentially of RT2 and RT3. In certain embodiments,the different ribotypes consist essentially of RT2 and not RT6. Incertain embodiments, the different ribotypes consist essentially of RT2and RT3. In certain embodiments, the different ribotypes consistessentially of RT3 and not RT6. In certain embodiments the mixture doesnot comprise ribotype RT6.

In certain embodiments, methods described herein comprise applying aneffective amount of a composition containing a plurality of microbes ofdifferent ribotypes. In certain embodiments, the plurality of microbesis a mixture of three or more P. acnes strains of different ribotypes.In certain embodiments, the mixture comprises RT1, RT2, and RT3. Incertain embodiments, the mixture comprises RT2, RT3, and not RT6. Incertain embodiments, the mixture comprises RT1, RT2, and RT6. In certainembodiments, the mixture comprises RT1, RT3, and not RT6. In certainembodiments, the mixture consists essentially of RT1, RT2, and RT3. Incertain embodiments, the mixture consists essentially of RT2, RT3, andnot RT6. In certain embodiments, the mixture consists essentially ofRT1, RT2, and not RT6. In certain embodiments, the mixture consistsessentially of RT1, RT3, and not RT6. In certain embodiments the mixturedoes not comprise RT6.

Methods described herein comprise applying probiotics of variousstrains. Compositions described herein comprise various strains ofbacteria. In certain embodiments, the strain has at least 50% homologyto a strain described herein. In certain embodiments, the strain has atleast 60% homology to a strain described herein. In certain embodiments,the strain has at least 70% homology to a strain described herein. Incertain embodiments, the strain has at least 80% homology to a straindescribed herein. In certain embodiments, the strain has at least 90%homology to a strain described herein. In certain embodiments, thestrain has at least 95% homology to a strain described herein. Incertain embodiments, the strain has at least 50% homology to SEQ ID NO:51, SEQ ID NO: 52, SEQ ID NO: 53, or SEQ ID NO: 54. In certainembodiments, the strain has at least 60% homology to SEQ ID NO: 51, SEQID NO: 52, SEQ ID NO: 53, or SEQ ID NO: 54. In certain embodiments, thestrain has at least 70% homology to SEQ ID NO: 51, SEQ ID NO: 52, SEQ IDNO: 53, or SEQ ID NO: 54. In certain embodiments, the strain has atleast 80% homology to SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53, orSEQ ID NO: 54. In certain embodiments, the strain has at least 90%homology to SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53, or SEQ ID NO:54. In certain embodiments, the strain has at least 95% homology to SEQID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53, or SEQ ID NO: 54. In certainembodiments, the strain has at least 99% homology to SEQ ID NO: 51, SEQID NO: 52, SEQ ID NO: 53, or SEQ ID NO: 54. In certain embodiments, thestrain has 100% homology to SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53,or SEQ ID NO: 54.

In certain embodiments, described herein, are methods for treating orpreventing acne comprising: administering an effective amount of ametabolite produced by a strain of P. acnes to a subject in needthereof. In certain embodiments, the metabolite is selected from thegroup comprising bacterial culture supernatant, cell lysate, proteins,nucleic acids, lipids, and other bacterial molecules. In certainembodiments, the metabolite is selected from the group comprisingbacterial culture supernatant, cell lysate, proteins, nucleic acids,lipids, and other bacterial molecules.

In some embodiments, compositions and methods disclosed herein maycomprise use of bacteria that does not comprise P. acnes bacteria, orthe application thereof, respectively. In some embodiments, the bacteriacomprises a Staphylococcus strain. In some embodiments, compositions andmethods disclosed herein may comprise use of fungus, such as Malassezia.

In some embodiments, described herein, methods for treating orpreventing acne comprising: administering an effective amount ofbacteria associated with healthy or normal skin. Healthy or normal skinmay be skin essentially free of acne. In some embodiments, describedherein, methods for treating or preventing acne comprising:administering an effective amount of bacteria that produces low toabsent levels of pro-inflammatory mediators when co-incubated with asubject's keratinocytes.

In some embodiments, described herein, are methods for treating orpreventing acne comprising: administering an effective amount of abacterium that does not induce expression of RNA that encodespro-inflammatory proteins. In some embodiments, described herein,methods for treating or preventing acne comprising: administering aneffective amount of a bacterium that does not induce expression ofpro-inflammatory proteins. In some embodiments, described herein,methods for treating or preventing acne comprising: administering aneffective amount of a bacterium that does not induce activity ofpro-inflammatory proteins. In some embodiments, described herein,methods for treating or preventing acne comprising: administering aneffective amount of a bacterium that does not induce expression of RNAthat encodes pro-inflammatory proteins.

In some embodiments, described herein, are methods for treating orpreventing acne comprising: administering an effective amount of abacterium that does not increase expression of RNA that encodespro-inflammatory proteins. In some embodiments, described herein, aremethods for treating or preventing acne comprising: administering aneffective amount of a bacterium that does not increase expression ofpro-inflammatory proteins. In some embodiments, described herein,methods for treating or preventing acne comprising: administering aneffective amount of a bacterium that does not increase activity ofpro-inflammatory proteins.

In some embodiments, described herein, are methods for treating orpreventing acne comprising: administering an effective amount of abacterium that does not increase expression of RNA that encodespro-inflammatory proteins to a level that they would cause or increaseacne when the bacterium is applied to a subject. In some embodiments,described herein, are methods for treating or preventing acnecomprising: administering an effective amount of a bacterium that doesnot increase expression of pro-inflammatory proteins to a level thatthey would cause or increase acne when the bacterium is applied to asubject. In some embodiments, described herein, methods for treating orpreventing acne comprising: administering an effective amount of abacterium that does not increase activity of pro-inflammatory proteinsto a level that they would cause or increase acne when the bacterium isapplied to a subject. Non-limiting examples of pro-inflammatory proteinsinclude IL-8, IL-1, IL-6, TNF-alpha, INF-alpha, and human beta defensin.

In some embodiments, described herein, are methods for treating orpreventing seborrheic dermatitis comprising: administering an effectiveamount of a health-associated strain of Propionibacterium to a subjectin need thereof. In some embodiments, described herein, are methods fortreating or preventing seborrheic dermatitis comprising: administeringan effective amount of a health-associated strain of P. acnes to asubject in need thereof. In some embodiments, the methods are performedafter the subject has undergone a cosmetic hair treatment (e.g., hairdye). In some embodiments, the effective amount is an amount thatresults in greater than about 55% Propionibacterium on an affected areaof the scalp or skin of the subject. In some embodiments, the effectiveamount is an amount that results in greater than about 60%Propionibacterium on an affected area of the scalp or skin of thesubject. In some embodiments, the effective amount is an amount thatresults in greater than about 65% Propionibacterium on an affected areaof the scalp or skin of the subject. In some embodiments, the effectiveamount is an amount that results in greater than about 70%Propionibacterium on an affected area of the scalp or skin of thesubject. In some embodiments, the effective amount is an amount thatresults between about 55% Propionibacterium and about 75%Propionibacterium on an affected area of the scalp or skin of thesubject. In some embodiments, the effective amount is an amount thatresults between about 65% Propionibacterium and about 80%Propionibacterium on an affected area of the scalp or skin of thesubject. In some embodiments, the effective amount is an amount thatresults between about 70% Propionibacterium and about 80%Propionibacterium on an affected area of the scalp or skin of thesubject. In some embodiments, the effective amount is an amount thatresults between about 70% Propionibacterium and about 85%Propionibacterium on an affected area of the scalp or skin of thesubject. In some embodiments, the effective amount is an amount thatprovides a desirable ratio of Propionibacterium to Staphylococcus on thescalp or skin of the subject. The desirable ratio of Propionibacteriumto Staphylococcus may be selected from about 2:1, about 2.5:1, about3:1, about 3.5:1 and about 4:1. The desirable ratio of Propionibacteriumto Staphylococcus may be selected from at least about 2:1, at leastabout 2.5:1, at least about 3:1, at least about 3.5:1 and at least about4:1. The desirable ratio of Propionibacterium to Staphylococcus may bebetween about 1.5:1 and about 4:1. The desirable ratio ofPropionibacterium to Staphylococcus may be between about 2:1 and about4:1. The desirable ratio of Propionibacterium to Staphylococcus may bebetween about 2.5:1 and about 4:1. The desirable ratio ofPropionibacterium to Staphylococcus may be between about 3:1 and about4:1. In some embodiments, an effective amount is an amount that providesa desirable amount of a Malassezia fungus.

In some embodiments, the methods of treating disclosed herein furthercomprise determining strains of bacteria on the skin of the subject thatcause or promote inflammation of the skin of the subject. In someembodiments, methods comprise assessing an inflammatory mediatedresponse in a sample of keratinocytes. In some embodiments, methodscomprise assessing an inflammatory mediated response in a sample ofkeratinocytes obtained from a subject. The subject may be a healthysubject. The subject may be a subject to be treated, such as a subjectsuffering from acne. In some embodiments, the methods comprise poolingor culturing keratinocytes from multiple subjects.

Methods disclosed herein may comprise administering a drug to thesubject. In some embodiments, the drug is administered orally. In someembodiments, the drug is administered topically. In some embodiments,the drug is administered topically to the skin of the subject that isaffected by acne. In certain embodiments, described herein, are methodsfor preventing or treating acne in a subject comprising: administeringan effective amount of a drug specifically targeting P. acnes. Incertain embodiments, described herein, are methods for preventing ortreating acne in a subject comprising: administering an effective amountof a drug targeting P. acnes of a ribotype selected from RT1, RT2, RT3,RT4, RT5, RT7, RT8, RT9, and RT10, and combinations thereof. In certainembodiments, described herein, are methods for preventing or treatingacne in a subject comprising: administering an effective amount of adrug targeting P. acnes of a ribotype selected from RT1, RT2, RT3, RT7,RT8, RT9, and RT10, and combinations thereof. In certain embodiments,described herein, are methods for preventing or treating acne in asubject comprising: administering an effective amount of a drugtargeting a strain of bacteria or fungus that induces or promotesproduction of inflammatory mediators from a subject's keratinocytes whenco-incubated with a subject's keratinocytes. In certain embodiments,described herein, are methods for preventing or treating acne in asubject comprising: administering an effective amount of a drugtargeting a strain of bacteria or fungus that induces or promotesproduction of inflammatory mediators from a subject's keratinocytes whena factor produced by the bacteria or fungus is co-incubated with asubject's keratinocytes. Such drugs are disclosed herein, e.g., smallmolecules, antisense molecules, siRNA, biologics, antibodies, andcombinations thereof.

Methods disclosed herein may comprise performing laser therapy on theskin of the subject. In some embodiments, laser therapy is performedprior to administration of a drug or bacteria disclosed herein to asubject. In some embodiments, laser therapy is performed afteradministration of a drug or bacteria disclosed herein to a subject. Insome embodiments, laser therapy is performed simultaneously withadministration of a drug or bacteria disclosed herein to a subject. Thelaser therapy may be a blue or red-light laser targeting porphyrins.

Compositions disclosed herein may be administered, daily, weekly, ormonthly. In certain embodiments, the composition is administered twicedaily. In certain embodiments, the composition is administered at leasttwice weekly. In certain embodiments, the composition is administered atleast twice monthly.

Combination Treatments

It is envisioned that the any of the compositions, health-associatedmicrobes or probiotics disclosed herein can be used in combination withother standard treatments. For example, in some embodiments, methodscomprise administering compositions disclosed herein before, after, orsimultaneously with administration of an additional therapeutic agent.In some embodiments, the methods may comprise topically administering anantibiotic. Non-limiting examples of topical antibiotics includeclindamycin, doxycycline, erythromycin, and tetracycline. In someembodiments, the methods may comprise orally administering anantibiotic. Non-limiting examples of oral antibiotics includeerythromycin; or a tetracycline, such as doxycycline or minocycline.Other standard treatments may comprise administering ananti-inflammatory agent, an antioxidant, an acid, light therapy, or acombination thereof.

In some embodiments, methods comprise treating the subject with a laser.In some embodiments, methods comprise treating the subject with bluelight. In some embodiments, methods comprise treating the subject withred light. In some embodiments, methods comprise treating the subjectwith a targeted laser device and/or active ingredient directed to atleast one pro-inflammatory strain of P. acnes. In some embodiments,methods comprise treating with a laser that targets porphyrins.

Treatment of Acne and Other Disorders with Microbiome Transplant

In certain embodiments, described herein, are methods to treat skindisorders comprising administering a microbiome transplant from ahealthy donor or a donor unaffected by a disease to a subject in needthereof. In certain embodiments, described herein, are methods to treatskin disorders comprising administering a microbiome transplant from ahealthy donor unaffected by a skin disorder. In certain embodiments, theskin disorder is acne. In certain embodiments, the skin disorder isselected from acne, eczema, psoriasis, seborrheic dermatitis, rosacea,autoimmune disease, lichen sclerosis, lichen planus, pruritus, prurigonodularis, lichen simplex chronicus, and a combination thereof.

In a certain embodiments, the disclosure provides method for obtainingand purifying a microbiome from a stool sample of a healthy individual,wherein the healthy individual is a first subject not suffering fromacne or any other skin disorder, and transplanting that to a secondsubject that suffers from a skin disorder. The skin disorder may beselected from acne, eczema, psoriasis, seborrheic dermatitis, rosacea,autoimmune disease such as lupus, bullous pemphigoid, pemphigus, lichenplanus, pruritus, and xerosis. In another embodiment, the disclosureprovides a method for obtaining and purifying a microbiome from an oralsample of a healthy individual not suffering from an inflammatorydisorder, and transplanting that to a subject that suffers from a skindisorder. Non-limiting examples of inflammatory conditions includeautoimmune disease (e.g., vitiligo, pernicious anemia, alopecia areata,pemphigus, pemphigoid, lupus, scleroderma, diabetes), atherosclerosis,and arthritis.

Diagnosis of Acne and Other Diseases

Health-associated P. acnes can be differentiated from disease-associatedP. acnes based on genetic differences. For example, disease-associatedP. acnes have been shown to harbor genomic elements that encode formultiple virulence genes. Many health-associated P. acnes, on the otherhand, carry clustered regularly interspaced short palindromic repeat(CRISPR) elements that prevent health-associated P. acnes from acquiringvirulence genes. In addition to genetic differences, an increase in P.acnes derived molecules such as porphyrins, proteases, lipases, andhemolysins, may be associated with disease. Therefore, genes encodingfor biosynthesis of P. acnes derived molecules (e.g., porphyrins,proteases, lipase, and hemolysins) may be useful to distinguish betweenhealth-associated P. acnes and disease-associated P. acnes.

In one aspect, provided herein are methods of differentiatinghealth-associated P. acnes bacteria from disease-associated P. acnesbacteria based on genetic markers. Exemplary methods comprise measuringexpression of one or more genetic markers including, but not limited to,deoR, Cas5, pIMPLE, type I lipase, type II lipase, and alaninedehydrogenase. In some instances, methods for differentiating betweenhealth-associated P. acnes and disease-associated P. acnes comprisedifferentiation based on ribotype. Also provided herein are methods ofdifferentiating between health-associated P. acnes anddisease-associated P. acnes comprising quantitative PCR or sequencing ofat least one genetic marker, such as, deoR, Cas5, pIMPLE, type I lipase,type II lipase, alanine dehydrogenase, or a combination thereof. In somecases, methods comprise differentiating between strains and/or ribotypesof P. acnes bacteria. As a non-limiting example, P. acnes RT6 comprisesa DNA-binding response regulator and/or phosphoglycerate kinase, whichis absent in RT1, RT2, RT3, RT4, and RT5. As another example, an ABCtransporter gene is absent from RT6 and present in RT1, RT2, RT3, RT4,and RT5. In some cases, such methods are used to select for bacteria foruse in a probiotic described herein. For example, RT6 is not present ina probiotic. In some cases, such methods are used to monitor treatmentof an individual with the probiotic. Moreover, in some cases, themethods are used to distinguish between a health-associated anddisease-associated bacteria of the same ribotype. For example, P. acnesRT1 has both a disease-associated and health-associated P. acnes thatare distinguishable based on the presence and/or absence of geneticmarkers.

Methods of diagnosing and/or monitoring treatment of a disease in anindividual comprising quantifying health-associated and/ordisease-associated P. acnes in a sample from the individual are alsoprovided. Certain methods for quantification as provided herein comprisemeasuring at least one of deoR, a CRISPR-associated protein, pIMPLE,type I lipase, type II lipase, alanine dehydrogenase, DNA-bindingresponse regulator, phosphoglycerate kinase, and ABC transporter. 23 Sribosomal RNA may be measured to determine quantity of total bacteria ina sample. In some embodiments, the treatment comprises administration ofa health-associated microbe or probiotic provided herein. As anon-limiting example, the probiotic comprises a P. acnes of RT1 and RT2.In some cases, the probiotic does not comprise a P. acnes of RT6.

Further provided herein are methods for determining a microbiome profilein an individual by detecting and/or quantifying at least one of deoR, aCRISPR-associated protein, pIMPLE, type I lipase, type II lipase,alanine dehydrogenase, DNA-binding response regulator, phosphoglyceratekinase, and ABC transporter in a sample from the individual. Fordetermining relative quantities of bacteria in a sample, 23S ribosomalRNA sequences may be used to estimate total bacteria in a sample fromthe individual. Determination of a microbiome profile may be usefulbefore and/or during treatment, for example, treatment with a probioticor health-associated bacteria, such as P. acnes. Methods for monitoringa treatment regimen following determination of a microbiome profile arealso provided.

Further provided are methods of diagnosing or characterizing acne orother skin disorders in an individual. Such methods may be combined withthe probiotics and bacterial compositions provided herein to assess forsuitability for treatment and/or treatment monitoring. In certainembodiments, the disease is acne. In certain embodiments, the skindisorder is acne, eczema, psoriasis, seborrheic dermatitis, rosacea,autoimmune disease, lichen sclerosis, lichen planus, pruritus, prurigonodularis, lichen simplex chronicus, or a combination thereof. Incertain embodiments, an individual is diagnosed with acne if theindividual is determined to possess a pathogenic strain ofPropionibacterium acnes (P. acnes), Staphylococcus, or Malassezia fungi.In certain embodiments, the pathogenic strain of P. acnes comprises aribotype (RT) that is associated with acne. In certain embodiments, theacne associated strain of P. acnes is of a ribotype selected from RT1,RT 4, RT5, RT7, RT8, RT9, and RT10. In certain embodiments, the acneassociated strain of P. acnes is of a ribotype selected from RT 4, RT5,and RT8. In certain embodiments, the methods comprise diagnosing theindividual with acne if a presence of Staphylococcus bacteria isdetected in a sample of the subject. In certain embodiments, the methodscomprise diagnosing the individual with acne if a presence of Malasseziafungi is detected in a sample of the subject.

In certain embodiments, the disclosure provides a method comprising:obtaining a skin sample from a subject; optionally isolating bacterialDNA from the sample; using one or more primer sets to amplify the DNA;and analyzing the amplified DNA for the presence of a sequence having atleast 95% homology with at least one of SEQ ID NOs 1-10, 29-32 and82-434, wherein the subject is diagnosed as having acne if the presenceof a sequence having at least 95% homology with at least one of SEQ IDNOs 1-10, 29-32 and 82-434 exists. For example, the amplified DNA may beanalyzed for the presence of a sequence having at least 99% homologywith at least one of SEQ ID NOs 1-10, 29-32 and 82-434 and wherein thesubject is diagnosed as having acne if the presence of a sequence havingat least 99% homology with at least one of SEQ ID NOs 1-10, 29-32 and82-434 exists. As another example, the amplified DNA may be analyzed forthe presence of at least one of SEQ ID NOs 1-10, 29-32 and 82-434 andwherein the subject is diagnosed as having acne if the presence of atleast one of SEQ ID NOs 1-10, 29-32 and 82-434 exists.

In certain embodiments, methods comprise detecting or characterizing amicrobe in a sample of a subject. In some embodiments, the methodscomprise detecting the microbe in an ex vivo sample. In someembodiments, the methods comprise detecting the microbe in an in vivosample. An exemplary method comprises: obtaining a stool sample from thesubject; isolating bacterial DNA from the sample; amplifying DNAselected from 16S, ribosomal DNA, 18S ribosomal DNA, and/or 23Sribosomal DNA, sequencing the amplified DNA products; and typing theindividual's gut bacteria. In certain embodiments, are methods fordetermining whether a subject has acne comprising: obtaining a stoolsample from the subject; isolating bacterial DNA from the sample andwhole genome shotgun sequencing DNA in the sample. Another exemplarymethod comprises obtaining a swab of skin sample from the subject, suchas from the face, back or other affected area.

Biological Samples for Diagnosis

In certain embodiments, diagnosing an individual comprises obtaining abiological sample. In certain embodiments, the biological sample is askin sample or biopsy. In certain embodiments, the biological sample isa stool or fecal sample. In certain embodiments, the biological sampleis an oral or oral mucosal sample. In certain embodiments, thebiological sample is a swab, obtained using a cotton swab or othercompatible swab. In certain embodiments, the sample contains bacteria.In certain embodiments, the sample contains a fungus. In certainembodiments, the sample contains a virus. In certain embodiments, thevirus is a bacteriophage. In certain embodiments, the sample is storedafter it has been collected, but before additional steps are performed.In certain embodiments, storage occurs at less than 8° C. In certainembodiments, storage occurs at less than 4° C. In certain embodiments,storage occurs at less than 0° C. In certain embodiments, storage occursat less than −20° C. In certain embodiments, storage occurs at less than−70° C. In certain embodiments, this storage is in glycerol, glycol,dimethyl sulfoxide, growth media, nutrient broth or any combinationthereof. In certain embodiments, the sample is stored for at least about1, 2, 3, 4, 5, 6, or 7 days. In some embodiments, the sample is storedfor at least about 1, 2, 3, or 4 weeks. In some embodiments, the sampleis stored for at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 or 12months. In some embodiments, the sample is stored for up to about 1, 2,3, or 4 weeks. In some embodiments, the sample is stored for up to about1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 or 12 months.

In some embodiments, a composition disclosed herein is stable at roomtemperature (˜25° C.) for at least about one day. In some embodiments, acomposition disclosed herein is stable for at least about three days. Insome embodiments, a composition disclosed herein is stable for at leastabout six days. In some embodiments, a composition disclosed herein isstable for at least about nine days. In some embodiments, a compositiondisclosed herein is stable for at least about twelve days.

In some embodiments, compositions disclosed herein possess therapeuticactivity when applied to skin with a skin disorder. In some embodiments,compositions disclosed herein possess an initial therapeutic activity atthe time the composition is produced or packaged. In some embodiments, acomposition disclosed herein maintains its initial therapeutic activityat room temperature (˜25° C.) for at least about one day. In someembodiments, a composition disclosed herein maintains its initialtherapeutic activity for at least about three days. In some embodiments,a composition disclosed herein maintains its initial therapeuticactivity for at least about six days. In some embodiments, a compositiondisclosed herein maintains its initial therapeutic activity for at leastabout nine days. In some embodiments, a composition disclosed hereinmaintains its initial therapeutic activity for at least about twelvedays.

In some embodiments, a composition disclosed herein maintains at leastabout 90% of its initial therapeutic activity at room temperature (˜25°C.) for at least about one day. In some embodiments, a compositiondisclosed herein maintains at least about 90% of its initial therapeuticactivity for at least about three days. In some embodiments, acomposition disclosed herein maintains at least about 90% of its initialtherapeutic activity for at least about six days. In some embodiments, acomposition disclosed herein maintains at least about 90% of its initialtherapeutic activity for at least about nine days. In some embodiments,a composition disclosed herein maintains at least about 90% of itsinitial therapeutic activity for at least about twelve days.

In some embodiments, a composition disclosed herein maintains at leastabout 80% of its initial therapeutic activity at room temperature (˜25°C.) for at least about one day. In some embodiments, a compositiondisclosed herein maintains at least about 80% of its initial therapeuticactivity for at least about three days. In some embodiments, acomposition disclosed herein maintains at least about 80% of its initialtherapeutic activity for at least about six days. In some embodiments, acomposition disclosed herein maintains at least about 80% of its initialtherapeutic activity for at least about nine days. In some embodiments,a composition disclosed herein maintains at least about 80% of itsinitial therapeutic activity for at least about twelve days.

In some embodiments, a composition disclosed herein maintains at leastabout 70% of its initial therapeutic activity at room temperature (˜25°C.) for at least about one day. In some embodiments, a compositiondisclosed herein maintains at least about 70% of its initial therapeuticactivity for at least about three days. In some embodiments, acomposition disclosed herein maintains at least about 70% of its initialtherapeutic activity for at least about six days. In some embodiments, acomposition disclosed herein maintains at least about 70% of its initialtherapeutic activity for at least about nine days. In some embodiments,a composition disclosed herein maintains at least about 70% of itsinitial therapeutic activity for at least about twelve days.

In some embodiments, a composition disclosed herein maintains at leastabout 50% of its initial therapeutic activity at room temperature (˜25°C.) for at least about one day. In some embodiments, a compositiondisclosed herein maintains at least about 50% of its initial therapeuticactivity for at least about three days. In some embodiments, acomposition disclosed herein maintains at least about 50% of its initialtherapeutic activity for at least about six days. In some embodiments, acomposition disclosed herein maintains at least about 50% of its initialtherapeutic activity for at least about nine days. In some embodiments,a composition disclosed herein maintains at least about 50% of itsinitial therapeutic activity for at least about twelve days.

In some embodiments, the sample is cultured at a physiologicaltemperature suitable for bacterial growth such as 30° C., 31° C., 32°C., 33° C., 34° C., 35° C., 36° C., 37° C., 38° C., 39° C. or 40° C. Insome embodiments, the sample is cultured at about 35° C. to about 39° C.In some embodiments, the sample is cultured at about 36° C. to about 38°C. In some embodiments, the sample is cultured in a liquid growth media.In some embodiments, the sample is cultured on a solid growth media suchas an agar plate. In some embodiments, the plates are blood agar.

In certain embodiments, samples disclosed herein are processed furtherbefore analysis. In some embodiments, no extraction or processingprocedures are performed on the sample. In some embodiments, nucleicacid is extracted from the sample. In some embodiments, the nucleic acidis DNA. In some embodiments, the DNA is bacterial DNA. In someembodiments, the Bacterial DNA is 16S ribosomal DNA. In someembodiments, the Bacterial DNA is 18S ribosomal DNA. In someembodiments, the Bacterial DNA is 23S ribosomal DNA. In someembodiments, the nucleic acid is ribosomal DNA. In some embodiments, thenucleic acid is RNA. In some embodiments, the nucleic acid is ribosomalRNA. In certain embodiments, the nucleic acid is extracted using anytechnique that does not interfere with subsequent analysis. In certainembodiments, this technique uses alcohol precipitation using ethanol,methanol or isopropyl alcohol. In certain embodiments, this techniqueuses phenol, chloroform, or any combination thereof. In certainembodiments, this technique uses cesium chloride. In certainembodiments, this technique uses sodium, potassium or ammonium acetateor any other salt commonly used to precipitate DNA. In certainembodiments, this technique utilizes a column or resin based nucleicacid purification scheme such as those commonly sold commercially, onenon-limiting example would be the GenElute Bacterial Genomic DNA Kitavailable from Sigma Aldrich. In certain embodiments, after extractionthe nucleic acid is stored in water, Tris buffer, or Tris-EDTA bufferbefore subsequent analysis. In certain embodiments, this storage is lessthan 8° C. In certain embodiments, this storage is less than 4° C. Incertain embodiments, this storage is less than 0° C. In certainembodiments, this storage is less than −20° C. In certain embodiments,this storage is less than −70° C. In certain embodiments, the nucleicacid is stored for 1, 2, 3, 4, 5, 6, or 7 days. In some embodiments, thenucleic acid is stored for 1, 2, 3, or 4 weeks. In some embodiments, thenucleic acid is stored for 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 or 12months.

After the samples have been obtained and the relevant nucleic acidsisolated the nucleic acids are sequenced. In certain embodiments, thenucleic acid sequenced is bacterial DNA. In certain embodiments, thenucleic acid sequence is bacterial 16S ribosomal DNA. In certainembodiments, the nucleic acid sequence is bacterial 18S ribosomal DNA.In certain embodiments, the nucleic acid sequence is bacterial 23Sribosomal DNA. In certain embodiments, the nucleic acid sequenced isbacteriophage DNA. In certain embodiments, the sequence is determinedusing PCR. In certain embodiments, at least one primer used in the PCRhas a sequence that corresponds to SEQ ID NO: 11, SEQ ID NO: 12, SEQ IDNO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22,SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO:27 or SEQ ID NO: 28. In certain embodiments, the PCR used isquantitative. In certain embodiments, the PCR reaction utilizes aTaqman™ or a similar quantitative PCR technology. In certainembodiments, the sequencing is performed using the Sanger sequencingmethod. In certain embodiments, the sequencing involves the use of chainterminating dideoxynucleotides. In certain embodiments, the sequencinginvolves gel-electrophoresis. In certain embodiments, the sequencing isperformed using a next generation sequencing method. In certainembodiments, the method is pyrosequencing. In certain embodiments, themethod is ion semiconductor sequencing. In certain embodiments, themethod is sequencing by synthesis. In certain embodiments, the method issequencing by ligation. In certain embodiments, the method is singlemolecule real time sequencing.

After the nucleic acids are sequenced, in certain embodiments, describedherein diagnosis is made. In certain, embodiments, diagnosis requiresthe use of a computer, statistical analysis, statistical analysissoftware, sequence analysis software, or any combination thereof. Incertain embodiments, different organisms are identified. In certainembodiments, Malassezia fungi are identified. In certain embodiments,different strains of bacteria are identified during compiling of themicrobiome. In certain embodiments, Staphylococcus bacteria areidentified. In certain embodiments, different strains of P. acnes areidentified during compiling of the microbiome. In certain embodiments,different strains of P. acnes are identified based upon their 16Sribosomal sequence or ribotype. In certain embodiments, P. acnes areidentified as belonging to RT1-RT10. In certain embodiments, the P.acnes are identified as belonging to RT1, RT2, RT3, RT6, or anycombination thereof. In further embodiments, a diagnostic report may besent through or accessed by the internet. A diagnostic report may besent through the mail to a health care provider, physician, or patient.

In certain embodiments, this disclosure provides a method fordetermining the presence of antibiotic resistant bacteria in anindividual with acne comprising, obtaining a skin sample from anindividual, isolating bacterial DNA from the sample, amplifying therelevant regions of the 16S, 18S or 23S ribosomal RNA from the sample,sequencing the amplified DNA products and determining antibioticresistance to tetracycline and erythromycin/clindamycin classes ofantibiotics respectively. In certain embodiments, bacteria present on orisolated from an individual's skin is tested or determined to beresistant to antibiotics. In certain embodiments, the antibiotic iserythromycin. In certain embodiments, the antibiotic is clindamycin. Incertain embodiments, antibiotic resistance is determined from thesequence of the 16S, 18S or 23S ribosomal subtype.

Methods of Preserving Preparations of Propionibacterium

Provided herein, in some aspects, are methods of producing desiredpreparations of Propionibacterium. In some embodiments, the methodscomprise producing a desired preparation of at least one strain ofPropionibacterium. In some embodiments, the at least one strain is astrain of P. acnes. In some embodiments, the at least one strain is nota strain of P. acnes subsp. acnes. In some embodiments, the at least onestrain is a strain of P. avidum. In some embodiments, the at least onestrain is a strain of P. granulosum. In some embodiments, the at leastone strain is a strain of P. acnes subsp. defendens. In preferredembodiments, the strain of Propionibacterium is a health-associatedstrain, as described herein.

In some embodiments, methods comprise adding a sample of thePropionibacterium to a glycerol solution to produce a Propionibacteriumglycerol stock, and storing the Propionibacterium glycerol stock at atemperature of about 4° C. or less. Producing a desired preparation ofPropionibacterium may comprise at least one of cooling, freezing, andstoring a Propionibacterium sample, a composition thereof or a stockthereof.

By way of non-limiting example, methods are provided herein forproducing a desired preparation of a P. acnes bacteria comprising addinga sample of the Propionibacterium to a glycerol solution to produce aPropionibacterium glycerol stock, and storing the Propionibacteriumglycerol stock at a temperature of about 4° C. or less, wherein morethan about 50% of the Propionibacterium bacteria is viable when thePropionibacterium bacteria in the glycerol solution is brought toambient temperature.

Also by way of non-limited examples, methods are provided herein forproducing a desired preparation of preserved Propionibacterium, whereinabout 90% of said Propionibacterium is viable after sixty days ofstorage, said method comprising: adding a sample of Propionibacterium toa solution of about 50% glycerol to produce a Propionibacterium stock,freezing the Propionibacterium glycerol stock at −20° C., therebyforming said desired preparation wherein greater than about 90% of thesample of Propionibacterium are viable after a thawing of thePropionibacterium glycerol stock.

In some embodiments, methods comprise storing the Propionibacterium,wherein at least about 1% of the Propionibacterium is viable when thePropionibacterium in the glycerol solution is brought to ambienttemperature. In some embodiments, methods comprise storing thePropionibacterium, wherein at least about 5% of the Propionibacterium isviable when the Propionibacterium in the glycerol solution is brought toambient temperature. In some embodiments, methods comprise storing thePropionibacterium, wherein at least about 10% of the Propionibacteriumis viable when the Propionibacterium in the glycerol solution is broughtto ambient temperature. In some embodiments, methods comprise storingthe Propionibacterium, wherein at least about 15% of thePropionibacterium is viable when the Propionibacterium in the glycerolsolution is brought to ambient temperature. In some embodiments, methodscomprise storing the Propionibacterium, wherein at least about 20% ofthe Propionibacterium is viable when the Propionibacterium in theglycerol solution is brought to ambient temperature. In someembodiments, methods comprise storing the Propionibacterium, wherein atleast about 30% of the Propionibacterium is viable when thePropionibacterium in the glycerol solution is brought to ambienttemperature. In some embodiments, methods comprise storing thePropionibacterium, wherein at least about 40% of the Propionibacteriumis viable when the Propionibacterium in the glycerol solution is broughtto ambient temperature. In some embodiments, methods comprise storingthe Propionibacterium, wherein at least about 50% of thePropionibacterium is viable when the Propionibacterium in the glycerolsolution is brought to ambient temperature. In some embodiments, atleast about 60% of the Propionibacterium is viable when thePropionibacterium in the glycerol solution is brought to ambienttemperature. In some embodiments, at least about 70% of thePropionibacterium is viable when the Propionibacterium in the glycerolsolution is brought to ambient temperature. In some embodiments, atleast about 80% of the P. acnes bacteria is viable when thePropionibacterium in the glycerol solution is brought to ambienttemperature. In some embodiments, more than about 90% of thePropionibacterium are viable when the Propionibacterium in the glycerolsolution is brought to ambient temperature.

In some embodiments, methods comprise adding the Propionibacterium to aglycerol solution, wherein the glycerol solution is between about 5% andabout 75% glycerol. In some embodiments, methods comprise adding thePropionibacterium to a glycerol solution, wherein the glycerol solutionis between about 5% and about 65% glycerol. In some embodiments, methodscomprise adding the Propionibacterium to a glycerol solution, whereinthe glycerol solution is between about 5% and about 55% glycerol. Insome embodiments, methods comprise adding the Propionibacterium to aglycerol solution, wherein the glycerol solution is between about 5% andabout 45% glycerol. In some embodiments, methods comprise adding thePropionibacterium to a glycerol solution, wherein the glycerol solutionis between about 5% and about 35% glycerol. In some embodiments, methodscomprise adding the Propionibacterium to a glycerol solution, whereinthe glycerol solution is between about 5% and about 25% glycerol. Insome embodiments, methods comprise adding the Propionibacterium to aglycerol solution, wherein the glycerol solution is between about 25%and about 75% glycerol. In some embodiments, the glycerol solution isbetween about 30% and about 70% glycerol. In some embodiments, theglycerol solution is between about 35% and about 65% glycerol. In someembodiments, the glycerol solution is between about 40% and about 60%glycerol. In some embodiments, the glycerol solution is between about45% and about 50% glycerol. In some embodiments, the glycerol solutionis about 25% glycerol. In some embodiments, the glycerol solution isabout 30% glycerol. In some embodiments, the glycerol solution is about35% glycerol. In some embodiments, the glycerol solution is about 40%glycerol. In some embodiments, the glycerol solution is about 45%glycerol. In some embodiments, the glycerol solution is about 50%glycerol. In some embodiments, the glycerol solution is about 55%glycerol. In some embodiments, the glycerol solution is about 60%glycerol.

In some embodiments, methods comprise storing Propionibacterium, or acomposition thereof, disclosed herein, at a selected temperature. Insome embodiments, methods comprise storing the Propionibacteriumglycerol stock at a selected temperature. In some embodiments, thetemperature is between about 30° C. and about −80° C. In someembodiments, the temperature is between about 25° C. and about −80° C.In some embodiments, the temperature is between about 25° C. and about−20° C. In some embodiments, the temperature is between about 30° C. andabout 4° C. In some embodiments, the temperature is between about 10° C.and about −80° C. In some embodiments, the temperature is between about10° C. and about −40° C. In some embodiments, the temperature is betweenabout 10° C. and about −30° C. In some embodiments, the temperature isbetween about 10° C. and about −20° C. In some embodiments, thetemperature is between about 4° C. and about −80° C. In someembodiments, the temperature is between about 4° C. and about −25° C. Insome embodiments, the temperature is between about 4° C. and about −20°C. In some embodiments, the temperature is about 22° C. to about 28° C.In some embodiments, the temperature is about 25° C. In someembodiments, the temperature is about 4° C. In some embodiments, thetemperature is about −20° C. In some embodiments, the temperature isbetween about −80° C.

In some embodiments, methods comprise thawing a composition ofPropionibacterium disclosed herein. In some embodiments, methodscomprise warming a composition of Propionibacterium bacteria disclosedherein. In some embodiments, methods comprise thawing aPropionibacterium glycerol stock at room temperature. In someembodiments, methods comprise rapid thawing the Propionibacteriumglycerol stock in a bath. The bath temperature may be between about 25°C. and about 40° C. In some embodiments, methods comprise rapidlythawing a composition of Propionibacterium bacteria disclosed herein. Byway of non-limiting example, a subject may apply a composition disclosedherein, wherein the composition is frozen, directly to skin. In someembodiments, methods comprise slowly thawing a composition ofPropionibacterium bacteria disclosed herein. By way of non-limitingexample, a subject may transfer a composition disclosed herein that isfrozen to a refrigerator to reach a refrigerated temperature beforebeing brought to room temperature, before being applied to skin, orbefore being combined with another composition (e.g., emollient, lotion,gel). The term “frozen” includes compositions at temperatures at whichthe composition is in a solid form or semi-solid form. Frozen mayinclude compositions at temperatures of less than 0° C., and less than−15° C. The term “refrigerated temperature” refers to a temperature ofabout 0° C. to about 10° C., e.g., 4° C. A refrigerated temperature doesnot necessarily need to be achieved with a refrigerator. By non-limitingexample, an ice bucket could similarly cool a sample.

In some embodiments, methods comprise storing a Propionibacteriumglycerol stock, wherein at least about 60% to at least about 90% of thePropionibacterium sample is viable after the Propionibacterium glycerolstock is brought to ambient temperature. In some embodiments, the atleast about 70% to at least about 90% of the P. acnes sample is viableafter the Propionibacterium glycerol stock is brought to ambienttemperature. In some embodiments, the at least about 80% to at leastabout 90% of the viable after the Propionibacterium glycerol stock isbrought to ambient temperature. In some embodiments, at least about 60%of Propionibacterium sample is viable after the Propionibacteriumglycerol stock is brought to ambient temperature. In some embodiments,at least about 70% of the P. acnes sample is viable after thePropionibacterium glycerol stock is brought to ambient temperature. Insome embodiments, at least about 80% of the Propionibacterium sample isviable after the Propionibacterium glycerol stock is brought to ambienttemperature. In some embodiments, at least about 90% of the P. acnessample is viable after the Propionibacterium glycerol stock is broughtto ambient temperature. Ambient temperature is considered an acceptableroom temperature. In some embodiments, the ambient temperature isbetween about 25° C. and about 35° C. In some embodiments, the ambienttemperature is between about 20° C. and about 30° C. In someembodiments, the ambient temperature is between about 22° C. and about28° C. In some embodiments, the ambient temperature is about 25° C.

In some embodiments, methods comprise storing a Propionibacteriumglycerol stock, wherein at least about 50% of the Propionibacteriumsample is viable after at least about 30 days of storing. In someembodiments, at least about 60% of the Propionibacterium sample isviable after at least about 30 days of storing. In some embodiments, atleast about 70% of the Propionibacterium sample is viable after at leastabout 20 days of storing. In some embodiments, at least about 80% of thePropionibacterium sample is viable after at least about 30 days ofstoring. In some embodiments, at least about 90% of thePropionibacterium sample is viable after at least about 30 days ofstoring. In some embodiments, at least about 95% of thePropionibacterium sample is viable after at least about 30 days ofstoring. In some embodiments, at least about 50% of thePropionibacterium sample is viable after at least about 60 days ofstoring. In some embodiments, at least about 60% of thePropionibacterium sample is viable after at least about 60 days ofstoring. In some embodiments, at least about 70% of the P. acnes sampleis viable after at least about 60 days of storing. In some embodiments,at least about 80% of the Propionibacterium sample is viable after atleast about 60 days of storing. In some embodiments, at least about 90%of the Propionibacterium sample is viable after at least about 60 daysof storing. In some embodiments, at least about 95% of thePropionibacterium sample is viable after at least about 60 days ofstoring. In some embodiments, at least about 50% of thePropionibacterium sample is viable after at least about 90 days ofstoring. In some embodiments, at least about 60% of thePropionibacterium sample is viable after at least about 90 days ofstoring. In some embodiments, at least about 70% of thePropionibacterium sample is viable after at least about 90 days ofstoring. In some embodiments, at least about 80% of thePropionibacterium sample is viable after at least about 90 days ofstoring. In some embodiments, at least about 90% of thePropionibacterium sample is viable after at least about 90 days ofstoring. In some embodiments, at least about 95% of thePropionibacterium sample is viable after at least about 90 days ofstoring. In some embodiments, at least about 50% of thePropionibacterium sample is viable after at least about 120 days ofstoring. In some embodiments, at least about 60% of thePropionibacterium sample is viable after at least about 120 days ofstoring. In some embodiments, at least about 70% of thePropionibacterium sample is viable after at least about 120 days ofstoring. In some embodiments, at least about 80% of thePropionibacterium sample is viable after at least about 120 days ofstoring. In some embodiments, at least about 90% of thePropionibacterium sample is viable after at least about 120 days ofstoring. In some embodiments, at least about 95% of thePropionibacterium sample is viable after at least about 120 days ofstoring. In some embodiments, at least about 50% of thePropionibacterium sample is viable after at least about 180 days ofstoring. In some embodiments, at least about 60% of thePropionibacterium sample is viable after at least about 180 days ofstoring. In some embodiments, at least about 70% of the sample is viableafter at least about 180 days of storing. In some embodiments, at leastabout 80% of the Propionibacterium sample is viable after at least about180 days of storing. In some embodiments, at least about 90% of thePropionibacterium sample is viable after at least about 180 days ofstoring. In some embodiments, at least about 95% of thePropionibacterium sample is viable after at least about 180 days ofstoring. In some embodiments, at least about 50% of thePropionibacterium sample is viable after at least about a year ofstoring. In some embodiments, at least about 60% of thePropionibacterium sample is viable after at least about a year ofstoring. In some embodiments, at least about 70% of thePropionibacterium sample is viable after at least about a year ofstoring. In some embodiments, at least about 80% of thePropionibacterium sample is viable after at least about a year ofstoring. In some embodiments, at least about 90% of thePropionibacterium sample is viable after at least about a year ofstoring. In some embodiments, at least about 95% of thePropionibacterium sample is viable after at least about a year ofstoring.

In some embodiments, methods comprise storing Propionibacterium in asolution, wherein the solution is between about 10% glycerol v/v andabout 90% glycerol v/v in solution. In some embodiments, the solution isbetween about 20% glycerol v/v and about 80% glycerol v/v in solution.In some embodiments, the solution is between about 25% glycerol v/v andabout 75% glycerol v/v in solution. In some embodiments, the solution isbetween about 30% glycerol v/v and about 70% glycerol v/v in solution.In some embodiments, the solution is between about 35% glycerol v/v andabout 65% glycerol v/v in solution. In some embodiments, the solution isbetween about 40% glycerol v/v and about 60% glycerol v/v in solution.In some embodiments, the solution is between about 45% glycerol v/v andabout 55% glycerol v/v in solution. In some embodiments, the solution isbetween about 15% glycerol v/v and about 35% glycerol v/v in solution.In some embodiments, the solution is between about 20% glycerol v/v andabout 30% glycerol v/v in solution. In some embodiments, the solution isabout 20% glycerol v/v in solution. In some embodiments, the solution isabout 25% glycerol v/v in solution. In some embodiments, the solution isabout 30% glycerol v/v in solution. In some embodiments, the solution isabout 35% glycerol v/v in solution. In some embodiments, the solution isabout 40% glycerol v/v in solution. In some embodiments, the solution isabout 45% glycerol v/v in solution. In some embodiments, the solution isabout 50% glycerol v/v in solution. In some embodiments, the solution isabout 50% glycerol v/v in solution. In some embodiments, the solution isabout 55% glycerol v/v in solution. In some embodiments, the solution isabout 60% glycerol v/v in solution. In some embodiments, the solution isabout 65% glycerol v/v in solution. In some embodiments, the solution isabout 75% glycerol v/v in solution.

In some embodiments, methods comprise storing Propionibacterium bacteriain a solution, wherein the solution comprises glycerol and water. Insome embodiments, the solution consists essentially of glycerol andwater. In some embodiments, methods comprise storing Propionibacteriumin a solution, wherein the solution comprises glycerol and a salinesolution. In some embodiments, the solution consists essentially ofglycerol and a saline solution. In some embodiments, the solutioncomprises glycerol and a buffered saline solution. In some embodiments,the solution consists essentially of glycerol and a buffered salinesolution. In some embodiments, the solution comprises glycerol and abuffered solution. In some embodiments, the buffered solution comprisessodium bicarbonate, citric acid or triethanolamine. In some embodiments,the solution comprises glycerol and a phosphate buffered salinesolution. In some embodiments, the solution consists essentially ofglycerol and a phosphate buffered saline solution.

In some embodiments, methods comprise storing Propionibacterium in asolution, wherein the solution has a pH of between about 3.5 and about7. In some embodiments, the solution has a pH of between about 4 andabout 6.5. In some embodiments, the solution has a pH of between about 4and about 6. In some embodiments, the solution has a pH of between about4 and about 5.5. In some embodiments, the solution has a pH of betweenabout 4.5 and about 5.5. In some embodiments, the solution has a pH ofbetween about 4.8 and about 5. In some embodiments, the solution has apH of about 4. In some embodiments, the solution has a pH of about 4.2.In some embodiments, the solution has a pH of about 4.4. In someembodiments, the solution has a pH of about 4.6. In some embodiments,the solution has a pH of about 4.8. In some embodiments, the solutionhas a pH of about 5. In some embodiments, the solution has a pH of about5.2. In some embodiments, the solution has a pH of about 5.4. In someembodiments, the solution has a pH of about 5.6. In some embodiments,the solution has a pH of about 5.8. In some embodiments, the solutionhas a pH of about 6.

In some embodiments, methods comprise storing Propionibacterium in asolution, wherein the solution comprises a salt or ion thereof. In someembodiments, the solution comprises an ion selected from potassium,calcium, magnesium, sodium, and boron. In some embodiments, the solutioncomprises potassium. In some embodiments, the solution comprisespotassium. In some embodiments, the concentration of the salt or ionthereof is between about 0.001 mM and about 1 mM. In some embodiments,the concentration of the salt or ion thereof is between about 0.001 mMand about 0.1 mM. In some embodiments, the concentration of the salt orion thereof is between about 0.01 mM and about 0.1 mM. In someembodiments, the concentration of the salt or ion thereof is betweenabout 0.05 mM and about 0.1 mM. In some embodiments, the concentrationof the salt or ion thereof is between about 0.01 mM and about 1 mM. Insome embodiments, the concentration of the salt or ion thereof isbetween about 0.1 mM and about 1 mM. In some embodiments, theconcentration of the salt or ion thereof is between about 100 mM andabout 250 mM. In some embodiments, the concentration of the salt or ionthereof is between about 125 mM and about 225 mM. In some embodiments,the concentration of the salt or ion thereof is between about 150 mM andabout 200 mM. In some embodiments, the concentration of potassium isbetween about 100 mM and about 250 mM. In some embodiments, theconcentration of potassium is between about 125 mM and about 225 mM. Insome embodiments, the concentration of potassium is between about 150 mMand about 200 mM. In some embodiments, the solution comprises calcium ata concentration of about 0.001 mM to about 1 mM. In some embodiments,the solution comprises calcium at a concentration of about 0.01 mM toabout 0.5 mM. In some embodiments, the solution comprises calcium at aconcentration of about 0.05 mM to about 0.1 mM.

In some embodiments, methods comprise storing Propionibacterium in asolution, wherein the solution comprises a prebiotic stabilizing agent.In some embodiments, the prebiotic stabilizing agent is selected from apolysaccharide or oligosaccharide. In some embodiments, the prebioticstabilizing agent is inulin. In some embodiments, the stabilizing agentis present in the solution at a concentration of about 0.01% v/v toabout 1% v/v. In some embodiments, the stabilizing agent is present inthe solution at a concentration of about 0.01% v/v to about 0.5% v/v. Insome embodiments, the stabilizing agent is present in the solution at aconcentration of about 0.05% v/v to about 0.2% v/v. In some embodiments,the solution comprises inulin at a concentration of about 0.01% v/v toabout 1% v/v. In some embodiments, the solution comprises inulin at aconcentration of about 0.01% v/v to about 0.5% v/v. In some embodiments,the solution comprises inulin at a concentration of about 0.05% v/v toabout 0.2% v/v. For clarity, the term % v/v, as used herein, representthe percentage of a total volume of a solution that is represented by avolume of a component of the solution.

In some embodiments, methods comprise storing Propionibacterium in asolution, wherein the solution comprises an anti-acne agent, wherein theanti-acne agent is an agent that prevents, reduces or abolishes acne. Insome embodiments, the anti-acne agent is selected from a retinoid, avitamin, an antioxidant, a peroxide, an acid, an oil, an alcohol, anextract, and analogs thereof. For clarity, the term, “analog,” as usedherein, refers to a compound having a structure similar to that ofanother one, but differing from it by less than about 10% of the totalstructure. In some embodiments, the retinoid is selected from tretinoin,tazarotene, adapalene, and retinol. In some embodiments, the vitamin oranalog thereof is selected from a Vitamin A, Vitamin C, Vitamin D,Vitamin E, and calciptotriene. In some embodiments, the antioxidant isselected from Vitamin C and Vitamin E. peroxide is benzoyl peroxide. Insome embodiments, the acid is selected from salicylic acid, azaelicacid, trichloracetic acid, and glycolic acid. In some embodiments, thealcohol is selected from cetyl alcohol, stearyl alcohol, and cetearylalcohol. In some embodiments, the alcohol is selected from retinol (alsoknown as Vitamin A₁) and resveratrol. In some embodiments, the oil isselected from lavender oil, clary sage oil, juniper berry oil, bergamotoil, jojoba oil, rosemary oil, coconut oil, avocado oil, peppermint oil,and tea tree oil. In some embodiments, the oil is tea tree oil. In someembodiments, the extract is selected from an extract of aloe, garlic,amaranth, neem, coriander, lemon, basil, grapefruit, cucumber, grape,beet, green tea or a combination thereof. In some embodiments, theextract is a green tea extract.

In some embodiments, methods comprise storing Propionibacterium in asolution, wherein the solution is incorporated in a biologic stabilityplatform. In some embodiments, the biologic stability platformeliminates a need for temperature control, e.g., cold chain storage. Insome embodiments, the biologic storage platform comprises foam drying orfoam formation of the solution or glycerol stock solution. In someembodiments, the biologic stability platform comprises at least one of aglyconanoparticle, a liposome, a nanoparticle, trehalose, sucrose,stachyose, hydroxyethyl starch, and a combination of glycine andmannitol.

In some embodiments, methods comprise storing or preserving a sample ofP. acnes of at least one selected ribotype. the sample of P. acnesbacteria comprises P. acnes bacteria of ribotype RT1. In someembodiments, the sample of P. acnes bacteria comprises P. acnes bacteriaof ribotype RT2. In some embodiments, the sample of P. acnes bacteriacomprises P. acnes bacteria of ribotypes RT1 and RT2. In someembodiments, the sample of P. acnes bacteria consists essentially of P.acnes bacteria of ribotype RT1. In some embodiments, the sample of P.acnes bacteria consists essentially of P. acnes bacteria of ribotypeRT2. In some embodiments, the sample of P. acnes bacteria consistsessentially of P. acnes bacteria of ribotypes RT1 and RT2.

In some embodiments, methods may comprise culturing an initial cultureof the sample of P. acnes bacteria. The initial culture may be a smalleraliquot of the Propionibacterium and the method may compriseproliferating the Propionibacterium to obtain a desired amount. In someembodiments, methods may comprise culturing the initial culture in aculture medium. In some embodiments, the cell culture medium comprisesreinforced clostridial medium. In some embodiments, the cell culturemedium consists essentially of reinforced clostridial medium. In someembodiments, the cell culture medium comprises Luria broth. In someembodiments, the cell culture medium comprises tryptone broth. In someembodiments, methods comprise at least one step of splitting, dilutingor passaging the initial culture or product thereof in the culturemedium. In some embodiments, the methods comprise at least one step ofwashing the sample of the initial culture or product thereof. In someembodiments, the methods comprise at least one step of centrifuging orpelleting the initial culture or product thereof. In some embodiments,the culture is centrifuged at about 3500 rcf to about 4500 rcf. In someembodiments, the culture is centrifuged at about 3800 rcf to about 4200rcf. In some embodiments, the culture is centrifuged at about 4000 rcf.In some embodiments, the methods comprise at least one step of vortexingthe initial culture or product thereof. In some embodiments, the methodscomprise at least one step of pipetting the initial culture of productthereof. Any one of the steps described herein may be performed at leastone time. Any one of the steps described herein may be performed twotimes. Any one of the steps described herein may be performed threetimes. In some embodiments, methods comprise adding a sachet to aculture comprising the sample of Propionibacterium or an initial culturethereof. In some embodiments the sachet reduces oxygen exposure to thePropionibacterium.

Compositions of Preserved Propionibacterium

Provided herein, in some aspects, are compositions that comprise apreserved sample of bacteria, wherein the bacteria comprisesPropionibacterium. In some embodiments, compositions disclosed hereincomprise P. acnes bacteria of ribotype RT1. In some embodiments, thecompositions comprise P. acnes bacteria of ribotype RT2. In someembodiments, the compositions comprise P. acnes bacteria of ribotype RT1and RT2. In some embodiments, the bacteria of the compositions consistessentially of P. acnes bacteria of ribotype RT1. In some embodiments,the bacteria of the compositions consist essentially of P. acnesbacteria of ribotype RT2. In some embodiments, the compositions compriseP. acnes bacteria of ribotype RT1 and RT2.

In some embodiments, compositions disclosed herein comprise a sample ofbacteria preserved in at least one cryopreservative agent. In someembodiments, the cryopreservative agent is a polyol. Non-limitingexamples of polyols include DMSO, ethylene glycol, glycerol, propylene(PEG) glycol, sucrose, trehalose, and 2-Methyl-2,4-pentanediol (MPD). Invarious embodiments, the PEG may have a molecular weight between about10 g/mol and about 10,000 g/mol. In various embodiments, the PEG mayhave a molecular weight between about 10 g/mol and about 5,000 g/mol. Invarious embodiments, the PEG may have a molecular weight between about10 g/mol and about 1,000 g/mol. In various embodiments, the PEG may havea molecular weight between about 10 g/mol and about 500 g/mol.

In some embodiments, compositions disclose herein comprise polyethyleneglycol. In some embodiments, a composition comprising polyethyleneglycol allows for a reduced amount of glycerol, whilst maintainingviability of bacteria in the composition that is similar to viability ofbacteria in compositions without polyethylene glycol and a greateramount of glycerol. In some embodiments, reducing or minimizing theamount of glycerol in a composition disclosed herein results in aformulation that has a texture that is more preferable to a subject. Insome embodiments, reducing or minimizing the amount of glycerol in acomposition disclosed herein results in a formulation that lesscomedogenic relative to a composition with a greater amount of glycerol.

In some embodiments, compositions disclosed herein comprise a sample ofbacteria preserved in a mixture of a first polyol and a second polyol.In some embodiments, the first polyol or the second polyol is glycerol.In some embodiments, the first polyol or the second polyol is apolyethylene glycol. In some embodiments, compositions disclosed hereincomprise a sample of bacteria preserved in a mixture of glycerol andpolyethylene glycol. In some embodiments, the mixture is between about1% glycerol v/v and about 50% glycerol v/v, and between about 1%polyethylene glycol w/v and about 50% w/v polyethylene glycol. In someembodiments, the mixture is between about 5% glycerol v/v and about 50%glycerol v/v, and between about 5% polyethylene glycol w/v and about 50%w/v polyethylene glycol. In some embodiments, the mixture is betweenabout 5% glycerol v/v and about 30% glycerol v/v, and between about 5%polyethylene glycol w/v and about 40% w/v polyethylene glycol. In someembodiments, the mixture is between about 10% glycerol v/v and about 35%glycerol v/v, and between about 10% polyethylene glycol w/v and about35% w/v polyethylene glycol.

In some embodiments, compositions disclose herein comprise a solution,wherein the solution is between about 1% glycerol v/v and about 75%glycerol v/v in solution. In some embodiments, the solution is betweenabout 1% glycerol v/v and about 50% glycerol v/v in solution. In someembodiments, the solution is between about 1% glycerol v/v and about 40%glycerol v/v in solution. In some embodiments, the solution is betweenabout 1% glycerol v/v and about 35% glycerol v/v in solution. In someembodiments, the solution is between about 1% glycerol v/v and about 30%glycerol v/v in solution. In some embodiments, the solution is betweenabout 1% glycerol v/v and about 25% glycerol v/v in solution. In someembodiments, the solution is between about 1% glycerol v/v and about 20%glycerol v/v in solution. In some embodiments, the solution is betweenabout 1% glycerol v/v and about 15% glycerol v/v in solution. In someembodiments, the solution is between about 5% glycerol v/v and about 50%glycerol v/v in solution. In some embodiments, the solution is betweenabout 5% glycerol v/v and about 40% glycerol v/v in solution. In someembodiments, the solution is between about 5% glycerol v/v and about 35%glycerol v/v in solution. In some embodiments, the solution is betweenabout 5% glycerol v/v and about 30% glycerol v/v in solution. In someembodiments, the solution is between about 5% glycerol v/v and about 25%glycerol v/v in solution. In some embodiments, the solution is betweenabout 10% glycerol v/v and about 40% glycerol v/v in solution. In someembodiments, the solution is between about 10% glycerol v/v and about35% glycerol v/v in solution. In some embodiments, the solution isbetween about 10% glycerol v/v and about 30% glycerol v/v in solution.In some embodiments, the solution is between about 10% glycerol v/v andabout 25% glycerol v/v in solution. In some embodiments, the solution isbetween about 15% glycerol v/v and about 40% glycerol v/v in solution.In some embodiments, the solution is between about 15% glycerol v/v andabout 35% glycerol v/v in solution. In some embodiments, the solution isbetween about 15% glycerol v/v and about 30% glycerol v/v in solution.In some embodiments, the solution is between about 15% glycerol v/v andabout 25% glycerol v/v in solution. In some embodiments, the solution isbetween about 20% glycerol v/v and about 50% glycerol v/v in solution.In some embodiments, the solution is between about 20% glycerol v/v andabout 40% glycerol v/v in solution. In some embodiments, the solution isbetween about 20% glycerol v/v and about 30% glycerol v/v in solution.

In some embodiments, compositions disclose herein comprise a solution,wherein the solution is between about 1% polyethylene glycol w/v andabout 75% polyethylene glycol w/v in solution. In some embodiments, thesolution is between about 1% polyethylene glycol w/v and about 50%polyethylene glycol w/v in solution. In some embodiments, the solutionis between about 1% polyethylene glycol w/v and about 40% polyethyleneglycol w/v in solution. In some embodiments, the solution is betweenabout 1% polyethylene glycol w/v and about 35% polyethylene glycol w/vin solution. In some embodiments, the solution is between about 1%polyethylene glycol w/v and about 30% polyethylene glycol w/v insolution. In some embodiments, the solution is between about 1%polyethylene glycol w/v and about 25% polyethylene glycol w/v insolution. In some embodiments, the solution is between about 1%polyethylene glycol w/v and about 20% polyethylene glycol w/v insolution. In some embodiments, the solution is between about 1%polyethylene glycol w/v and about 15% polyethylene glycol w/v insolution. In some embodiments, the solution is between about 5%polyethylene glycol w/v and about 50% polyethylene glycol w/v insolution. In some embodiments, the solution is between about 5%polyethylene glycol w/v and about 40% polyethylene glycol w/v insolution. In some embodiments, the solution is between about 5%polyethylene glycol w/v and about 35% polyethylene glycol w/v insolution. In some embodiments, the solution is between about 5%polyethylene glycol w/v and about 30% polyethylene glycol w/v insolution. In some embodiments, the solution is between about 5%polyethylene glycol w/v and about 25% polyethylene glycol w/v insolution. In some embodiments, the solution is between about 10%polyethylene glycol w/v and about 40% polyethylene glycol w/v insolution. In some embodiments, the solution is between about 10%polyethylene glycol w/v and about 35% polyethylene glycol w/v insolution. In some embodiments, the solution is between about 10%polyethylene glycol w/v and about 30% polyethylene glycol w/v insolution. In some embodiments, the solution is between about 10%polyethylene glycol w/v and about 25% polyethylene glycol w/v insolution. In some embodiments, the solution is between about 15%polyethylene glycol w/v and about 40% polyethylene glycol w/v insolution. In some embodiments, the solution is between about 15%polyethylene glycol w/v and about 35% polyethylene glycol w/v insolution. In some embodiments, the solution is between about 15%polyethylene glycol w/v and about 30% polyethylene glycol w/v insolution. In some embodiments, the solution is between about 15%polyethylene glycol w/v and about 25% polyethylene glycol w/v insolution. In some embodiments, the solution is between about 20%polyethylene glycol w/v and about 50% polyethylene glycol w/v insolution. In some embodiments, the solution is between about 20%polyethylene glycol w/v and about 40% polyethylene glycol w/v insolution. In some embodiments, the solution is between about 20%polyethylene glycol w/v and about 30% polyethylene glycol w/v insolution.

In some embodiments, the solution is about 5% glycerol v/v in solution.In some embodiments, the solution is about 10% glycerol v/v in solution.In some embodiments, the solution is about 15% glycerol v/v in solution.In some embodiments, the solution is about 20% glycerol v/v in solution.In some embodiments, the solution is about 25% glycerol v/v in solution.In some embodiments, the solution is about 30% glycerol v/v in solution.In some embodiments, the solution is about 35% glycerol v/v in solution.In some embodiments, the solution is about 40% glycerol v/v in solution.In some embodiments, the solution is about 45% glycerol v/v in solution.In some embodiments, the solution is about 50% glycerol v/v in solution.In some embodiments, the solution is about 55% glycerol v/v in solution.In some embodiments, the solution is about 60% glycerol v/v in solution.In some embodiments, the solution is about 70% glycerol v/v in solution.

In some embodiments, compositions disclosed herein comprise a solution,wherein the solution comprises glycerol and water. In some embodiments,the solution consists essentially of glycerol and water. In someembodiments, methods comprise storing Propionibacterium in a solution,wherein the solution comprises glycerol and a saline solution. In someembodiments, the solution consists essentially of glycerol and a salinesolution. In some embodiments, the solution comprises glycerol and abuffered saline solution. In some embodiments, the solution consistsessentially of glycerol and a buffered saline solution. In someembodiments, the solution comprises glycerol and a buffered solution. Insome embodiments, the buffered solution comprises sodium bicarbonate,citric acid or triethanolamine. In some embodiments, the solutioncomprises glycerol and a phosphate buffered saline solution. In someembodiments, the solution consists essentially of glycerol and aphosphate buffered saline solution.

In some embodiments, compositions disclosed herein comprise a solution,wherein the solution has a pH of between about 3.5 and about 7. In someembodiments, the solution has a pH of between about 4 and about 6.5. Insome embodiments, the solution has a pH of between about 4 and about 6.In some embodiments, the solution has a pH of between about 4 and about5.5. In some embodiments, the solution has a pH of between about 4.5 andabout 5.5. In some embodiments, the solution has a pH of between about4.8 and about 5. In some embodiments, the solution has a pH of about 4.In some embodiments, the solution has a pH of about 4.2. In someembodiments, the solution has a pH of about 4.4. In some embodiments,the solution has a pH of about 4.6. In some embodiments, the solutionhas a pH of about 4.8. In some embodiments, the solution has a pH ofabout 5. In some embodiments, the solution has a pH of about 5.2. Insome embodiments, the solution has a pH of about 5.4. In someembodiments, the solution has a pH of about 5.6. In some embodiments,the solution has a pH of about 5.8. In some embodiments, the solutionhas a pH of about 6.

In some embodiments, compositions disclosed herein comprise a solution,wherein the solution comprises a salt or ion thereof. In someembodiments, the solution comprises an ion selected from potassium,calcium, magnesium, sodium, and boron. In some embodiments, the solutioncomprises potassium. In some embodiments, the solution comprisespotassium. In some embodiments, the concentration of the salt or ionthereof is between about 0.001 mM and about 1 mM. In some embodiments,the concentration of the salt or ion thereof is between about 0.001 mMand about 0.1 mM. In some embodiments, the concentration of the salt orion thereof is between about 0.01 mM and about 0.1 mM. In someembodiments, the concentration of the salt or ion thereof is betweenabout 0.05 mM and about 0.1 mM. In some embodiments, the concentrationof the salt or ion thereof is between about 0.01 mM and about 1 mM. Insome embodiments, the concentration of the salt or ion thereof isbetween about 0.1 mM and about 1 mM. In some embodiments, theconcentration of the salt or ion thereof is between about 100 mM andabout 250 mM. In some embodiments, the concentration of the salt or ionthereof is between about 125 mM and about 225 mM. In some embodiments,the concentration of the salt or ion thereof is between about 150 mM andabout 200 mM. In some embodiments, the concentration of potassium isbetween about 100 mM and about 250 mM. In some embodiments, theconcentration of potassium is between about 125 mM and about 225 mM. Insome embodiments, the concentration of potassium is between about 150 mMand about 200 mM. In some embodiments, the solution comprises calcium ata concentration of about 0.001 mM to about 1 mM. In some embodiments,the solution comprises calcium at a concentration of about 0.01 mM toabout 0.5 mM. In some embodiments, the solution comprises calcium at aconcentration of about 0.05 mM to about 0.1 mM.

In some embodiments, compositions disclosed herein comprise a solution,wherein the solution comprises at least one stabilizing agent. In someembodiments, the stabilizing agent is selected from inulin, sucrose,trehalose, cornstarch, maltodextrin, guar guy, locust bean gum, andxanthan gum. In some embodiments, trehalose or sucrose stabilizesbacteria for cold-chain free stability. In some embodiments, thestabilizing agent is inulin. In some embodiments, the stabilizing agentis present in the solution at a concentration of about 0.01% v/v toabout 1% v/v. In some embodiments, the stabilizing agent is present inthe solution at a concentration of about 0.01% v/v to about 0.5% v/v. Insome embodiments, the stabilizing agent is present in the solution at aconcentration of about 0.05% v/v to about 0.2% v/v. In some embodiments,the solution comprises inulin at a concentration of about 0.01% v/v toabout 1% v/v. In some embodiments, the solution comprises inulin at aconcentration of about 0.01% v/v to about 0.5% v/v. In some embodiments,the solution comprises inulin at a concentration of about 0.05% v/v toabout 0.2% v/v.

In some embodiments, compositions disclosed herein comprise a solution,wherein the solution comprises an anti-acne agent, wherein the anti-acneagent is an agent that prevents, reduces or abolishes acne. In someembodiments, the anti-acne agent is selected from a retinoid, a vitamin,an antioxidant, a peroxide, an acid, an oil, an alcohol, an extract, andanalogs thereof. In some embodiments, the retinoid is selected fromtretinoin, tazarotene, adapalene, and retinol. In some embodiments, thevitamin or analog thereof is selected from Vitamin D, Vitamin C, VitaminE, and calciptotriene. In some embodiments, the antioxidant is selectedfrom Vitamin C and Vitamin E. peroxide is benzoyl peroxide. In someembodiments, the acid is selected from salicylic acid, azaelic acid,trichloracetic acid, and glycolic acid. In some embodiments, the alcoholis selected from retinol and resveratrol. In some embodiments, the oilis tea tree oil. In some embodiments, the extract is a green teaextract.

In some embodiments, compositions disclosed herein comprise a solution,wherein the solution is incorporated in a biologic stability platform.In some embodiments, the biologic stability platform eliminates a needfor temperature control, e.g., cold chain storage. In some embodiments,the biologic storage platform comprises foam drying or foam formation ofthe solution or glycerol stock solution. In some embodiments, thebiologic stability platform comprises at least one of aglyconanoparticle, a liposome, a nanoparticle, trehalose, sucrose,stachyose, hydroxyethyl starch, and a combination of glycine andmannitol.

In some embodiments, compositions disclosed herein have a temperature ofabout −80° C. to about 10° C. In some embodiments, the composition is ata temperature of about −80° C. to about 4° C. In some embodiments, thecomposition is at a temperature of about −40° C. to about 10° C. In someembodiments, the composition is at a temperature of about −25° C. toabout 10° C. In some embodiments, the composition is at a temperature ofabout −20° C. to about 4° C. In some embodiments, the composition is ata temperature of about −90° C. to about −70° C. In some embodiments, thecomposition is at a temperature of about −30° C. to about −10° C. Insome embodiments, the composition is at a temperature of about −80° C.In some embodiments, the composition is at a temperature of about −20°C. In some embodiments, the composition is at a temperature of about 4°C.

In some embodiments, compositions disclosed herein comprise aPropionibacterium glycerol stock, wherein at least about 60% to at leastabout 90% of the Propionibacterium sample is viable after thePropionibacterium glycerol stock is brought to ambient temperature. Insome embodiments, the at least about 70% to at least about 90% of thePropionibacterium sample is viable after the Propionibacterium glycerolstock is brought to ambient temperature. In some embodiments, the atleast about 80% to at least about 90% of the viable after thePropionibacterium glycerol stock is brought to ambient temperature. Insome embodiments, at least about 60% of the P. acnes sample is viableafter the Propionibacterium glycerol stock is brought to ambienttemperature. In some embodiments, at least about 70% of thePropionibacterium sample is viable after the Propionibacterium glycerolstock is brought to ambient temperature. In some embodiments, at leastabout 80% of the Propionibacterium sample is viable after thePropionibacterium glycerol stock is brought to ambient temperature. Insome embodiments, at least about 90% of the Propionibacterium sample isviable after the Propionibacterium glycerol stock is brought to ambienttemperature. Ambient temperature is considered an acceptable roomtemperature. In some embodiments, the ambient temperature is betweenabout 25° C. and about 35° C. In some embodiments, the ambienttemperature is between about 20° C. and about 30° C. In someembodiments, the ambient temperature is between about 22° C. and about28° C. In some embodiments, the ambient temperature is about 25° C.

In some embodiments, compositions disclosed herein comprise aPropionibacterium glycerol stock, wherein at least about 50% of thePropionibacterium sample is viable after at least about 30 days ofstoring. In some embodiments, at least about 60% of thePropionibacterium sample is viable after at least about 30 days ofstoring. In some embodiments, at least about 70% of the P. acnes sampleis viable after at least about 20 days of storing. In some embodiments,at least about 80% of the Propionibacterium sample is viable after atleast about 30 days of storing. In some embodiments, at least about 90%of the Propionibacterium sample is viable after at least about 30 daysof storing. In some embodiments, at least about 95% of thePropionibacterium sample is viable after at least about 30 days ofstoring. In some embodiments, at least about 50% of thePropionibacterium sample is viable after at least about 60 days ofstoring. In some embodiments, at least about 60% of thePropionibacterium sample is viable after at least about 60 days ofstoring. In some embodiments, at least about 70% of thePropionibacterium sample is viable after at least about 60 days ofstoring. In some embodiments, at least about 80% of thePropionibacterium sample is viable after at least about 60 days ofstoring. In some embodiments, at least about 90% of thePropionibacterium sample is viable after at least about 60 days ofstoring. In some embodiments, at least about 95% of thePropionibacterium sample is viable after at least about 60 days ofstoring. In some embodiments, at least about 50% of thePropionibacterium sample is viable after at least about 90 days ofstoring. In some embodiments, at least about 60% of thePropionibacterium sample is viable after at least about 90 days ofstoring. In some embodiments, at least about 70% of thePropionibacterium sample is viable after at least about 90 days ofstoring. In some embodiments, at least about 80% of thePropionibacterium sample is viable after at least about 90 days ofstoring. In some embodiments, at least about 90% of thePropionibacterium sample is viable after at least about 90 days ofstoring. In some embodiments, at least about 95% of thePropionibacterium sample is viable after at least about 90 days ofstoring. In some embodiments, at least about 50% of thePropionibacterium sample is viable after at least about 120 days ofstoring. In some embodiments, at least about 60% of thePropionibacterium sample is viable after at least about 120 days ofstoring. In some embodiments, at least about 70% of thePropionibacterium sample is viable after at least about 120 days ofstoring. In some embodiments, at least about 80% of thePropionibacterium sample is viable after at least about 120 days ofstoring. In some embodiments, at least about 90% of thePropionibacterium sample is viable after at least about 120 days ofstoring. In some embodiments, at least about 95% of thePropionibacterium sample is viable after at least about 120 days ofstoring. In some embodiments, at least about 50% of thePropionibacterium sample is viable after at least about 180 days ofstoring. In some embodiments, at least about 60% of thePropionibacterium sample is viable after at least about 180 days ofstoring. In some embodiments, at least about 70% of the sample is viableafter at least about 180 days of storing. In some embodiments, at leastabout 80% of the Propionibacterium sample is viable after at least about180 days of storing. In some embodiments, at least about 90% of thePropionibacterium sample is viable after at least about 180 days ofstoring. In some embodiments, at least about 95% of thePropionibacterium sample is viable after at least about 180 days ofstoring. In some embodiments, at least about 50% of thePropionibacterium sample is viable after at least about a year ofstoring. In some embodiments, at least about 60% of thePropionibacterium sample is viable after at least about a year ofstoring. In some embodiments, at least about 70% of thePropionibacterium sample is viable after at least about a year ofstoring. In some embodiments, at least about 80% of thePropionibacterium sample is viable after at least about a year ofstoring. In some embodiments, at least about 90% of thePropionibacterium sample is viable after at least about a year ofstoring. In some embodiments, at least about 95% of thePropionibacterium sample is viable after at least about a year ofstoring.

In some embodiments, compositions disclosed herein have a storage lifeof at least about thirty days to at least about ninety days. In someembodiments, the compositions disclosed herein have a storage life of atleast about 30 days to at least about 120 days. In some embodiments, thecompositions disclosed herein have a storage life of at least about 30days to at least about 180 days. In some embodiments, the compositionsdisclosed herein have a storage life of at least about thirty days toabout ninety days. In some embodiments, the compositions disclosedherein have a storage life of at least about 30 days to about 120 days.In some embodiments, the compositions disclosed herein have a storagelife of at least about 30 days to about 180 days. In some embodiments,the compositions disclosed herein have a storage life of at least aboutthirty days. In some embodiments, the compositions disclosed herein havea storage life of at least about sixty days. In some embodiments, thecompositions disclosed herein have a storage life of at least aboutninety days. In some embodiments, the compositions disclosed herein havea storage life of at least about 120 days. In some embodiments, thecompositions disclosed herein have a storage life of at least about 180days. In some embodiments, the compositions disclosed herein have astorage life of at least about 240 days. In some embodiments, thecompositions disclosed herein have a storage life of at least about oneyear. In some embodiments, the compositions disclosed herein have astorage life of up to about one year.

In some embodiments, the compositions disclosed herein are capable ofbeing thawed and subsequently applied to a subject in need thereof. Insome embodiments, the compositions disclosed herein are capable of beingwarmed and subsequently applied to a subject in need thereof. In someembodiments, the compositions disclosed herein are capable of beingrefrigerated and subsequently applied to a subject in need thereof. Insome embodiments, subsequently applied to the subject comprises applyingthe composition directly to the skin of the subject. In someembodiments, subsequently applied to the subject comprises applying thecomposition to an application composition before being applied to theskin. The application composition may be selected from a liquid, gel,lotion, emollient, paste, mask, and virtually any solution that can beapplied to the skin of a subject. In some embodiments, the applicationcomposition is free of any anti-acne agent. In some embodiments, theapplication composition comprises an anti-acne agent. In someembodiments, the compositions disclosed herein are capable of beingapplied directly from a frozen stock to skin of a subject withoutthawing or warming.

TABLE 8 Exemplary Sequences (Additional SEQ IDsprovided in sequence listing filed herewith).Bold characters highlight differences betweenType I lipase and Type II lipase. SEQ ID De- NO. scription Sequence 60Type I gtagatacagatacatctgaggagat lipase ccatgaagaaaaactggttactcacaaccctccttgccacaatgatgatcgc catgggcacgacgaccaccgccttcgccagcccgcctaccgacatcactccc gaacatccaggcggggttaccgcgcctcacagccccgacggaatcccctcga atattgaggggccaagtatgcccagctggacctctgcaatcaggttcgcaat gaagaaccccggcacgaaagtcccgggcaccaacgacttcacctgcaaaccg aggaaaggcacccatcccgtcgtgctcatcccgggcacatccgaggacgcct tcatcacgtggtcgtactacggtccccgccaggattctgcgcctacacgttc aactacaacccggaaacacatccgcttgtggaagccgctgagaccagcggca acatctactccacggcagctttcatggcccacttcgttgacagagtgctcaa ggcaaccggtgctcagaaggtcaacctcgtcggccattctcagggcggcggc cccctgccgcgcgcgtacatcaaatattacggggcgccaagaaagtcctcat ctcgtcggtttggttccttccaacaggggaacacgcatgctcggcctggaga agttcctcaatgccagcggaaacccgctcagcactatcttcaatgctgcagc acagtttcgaaagctggaatccctgccccaacagttgcaagactccacattt ctcagggaactcaacgcggatggaatgaccgtccccggcatcacatacaccg tcatcgccacccagttcgacaaccgagtatttccgtggactaataccttcat caatgagcccggggtcaagaacatcgtcatccaagacgtctgtcccttggac cacagcgcccacacggatatccctaggacccgatgacccttcagattgtcat caacgccttggaccccgagcgggccgccccggtcacctgcaccattcgccca ttcaggcccagttag 61 Type IIgcagatgcatctgagaagatccatga lipase agaaaaactggttactcacaaccctccttgccacaatgatgatcgccatggg cacgacgaccaccgccttcgccagcccgcctaccgacatcactcccgaacat ccaggcggggttacccgcctcacagccccgacggaatcccctcgaatattga ggggccaagtatgcccagctggacctctgcaatcaggttcgcaatgaagaac cccggcacgaaagtcccgggcaccaacgacttcacctgcaaaccgaggaaag gcacccatcccgtcgtgctcatcccgggcacatccgaggacgccttcatcac gtggtcgtactacggtccccgccaggattctgcgcctacacgttcaactaca acccggaaacacatccgcttgtggaagccgctgagaccagcggcaacatcta ctccacggcagctttcatggcccacttcgttgacagagtgctcaaggcaacc ggtgctcagaaggtcaacctcgtcggccattctcagggcggcggccccctgc cgcgcgcgtacatcaaatattacggggcgccaagaaagtcctcatctcgtcg gtttggttccttccaacaggggaacacgcatgctcggcctggagaagttcct caatgccagcggaaacccgctcagcactatcttcaatgctgcagcacagttt cgaaagctggaatccctgccccaacagttgcaagactccacatttctcaggg aactcaacgcggatggaatgaccgtccccggcatcacatacaccgtcatcgc cacccagttcgacaaccgagtatttccgtggactaataccttcatcaatgag cccggggtcaagaacatcgtcatccaagacgtctgtcccttggaccacagcg cccacacggatatccctaggacccgatgacccttcagattgtcatcaacgcc ttggaccccgagcgggccgccccggtcacctgcaccattcgcccattcaggc ccagttag

The disclosure is further understood through review of the numberedembodiments recited herein. Various embodiments contemplated herein mayinclude, but need not be limited to, one or more of the following, andcombinations thereof:

1. A pharmaceutical probiotic composition comprising: (a) atherapeutically effective amount of a health-associatedPropionibacterium acnes microbe, wherein the health-associatedPropionibacterium acnes microbe has been engineered or selected tocomprise at least one gene encoding at least one of a deoxyribose operonrepressor and a type II lipase, and less than about 10% pIMPLE plasmid;and (b) a pharmaceutically acceptable excipient or biologicalstabilizer. 2. The pharmaceutical probiotic composition of embodiment 1,wherein the health-associated Propionibacterium acnes microbe has beenengineered or selected to comprise a deoxyribose operon repressor and atype II lipase. 3. The pharmaceutical probiotic composition ofembodiment 1 or 2, wherein a Cas 5 protein is absent from thehealth-associated Propionibacterium acnes microbe. 4. The pharmaceuticalprobiotic composition of any one of embodiments 1-3, wherein thehealth-associated Propionibacterium acnes microbe comprises an RT1 orRT2 ribotype. 5. The pharmaceutical probiotic composition of any one ofembodiments 1-4, wherein the health-associated Propionibacterium acnesmicrobe does not comprise an RT6 ribotype. 6. The pharmaceuticalprobiotic composition of any one of embodiments 1-5, wherein thehealth-associated Propionibacterium acnes microbe comprises less thanabout 1% pIMPLE plasmid. 7. The pharmaceutical probiotic composition ofany one of embodiments 1-6, wherein the health-associatedPropionibacterium acnes microbe comprises less than about 0.3% pIMPLEplasmid. 8. The pharmaceutical probiotic composition of any one ofembodiments 1-7, wherein the health-associated Propionibacterium acnesmicrobe comprises a mixture of two or more different ribotypes ofPropionibacterium acnes. 9. The pharmaceutical probiotic composition ofany one of embodiments 1-8, wherein the pharmaceutically acceptableexcipient or biological stabilizer increases the viability of thehealth-associated Propionibacterium acnes microbe at a temperature fromabout −10° C. to about 30° C. 10. The pharmaceutical probioticcomposition of any one of embodiments 1-9, comprising at least one of anHP3A11 strain of P. acnes, an HP3B4 strain of P. acnes, an HP4G1 strainof P. acnes, or an HP5G4 strain of P. acnes. 11. The pharmaceuticalprobiotic composition of any one of embodiments 1-10, comprising atleast one additional strain of bacteria comprising Propionibacteriumavidum, Propionibacterium acnes subsp. defendens, or Propionibacteriumgranulosum. 12. The pharmaceutical probiotic composition of any one ofembodiments 1-11, wherein the health-associated Propionibacterium acnesmicrobe expresses an ATP binding cassette transporter. 13. Thepharmaceutical probiotic composition of any one of embodiments 1-12,wherein the health-associated Propionibacterium acnes microbe does notexpress a DNA binding response regulator or a phosphoglycerate kinase.14. A method of treating a skin disorder or condition comprisingapplying a therapeutically effective amount of a pharmaceuticalprobiotic composition comprising: (a) therapeutically effective amountof a health-associated Propionibacterium acnes microbe, wherein thehealth-associated Propionibacterium acnes microbe has been engineered orselected to comprise at least one gene encoding at least one of adeoxyribose operon repressor and a type II lipase, and less than about10% pIMPLE plasmid; and (b) a pharmaceutically acceptable excipient orbiological stabilizer. 15. The method of embodiment 14, wherein the skindisorder or condition comprises acne, eczema, seborrheic dermatitis,psoriasis, or rosacea. 16. The method of embodiment 14 or 15, whereinthe health-associated Propionibacterium acnes microbe has beenengineered or selected to at least one gene encoding the deoxyriboseoperon repressor and the type II lipase. 17. The method of any one ofembodiments 14-16, wherein a CRISPR locus or portion thereof is absentfrom the health-associated Propionibacterium acnes microbe. 18. Themethod of any one of embodiments 14-17, wherein the health-associatedPropionibacterium acnes microbe comprises an RT1 or RT2 ribotype. 19.The method of any one of embodiments 14-18, wherein thehealth-associated Propionibacterium acnes microbe does not comprise anRT6 ribotype. 20. The method of any one of embodiments 14-19, whereinthe health-associated Propionibacterium acnes microbe comprises lessthan about 1% pIMPLE plasmid. 21. The method of any one of embodiments14-20, wherein the health-associated Propionibacterium acnes microbecomprises less than about 0.3% pIMPLE plasmid. 22. The method of any oneof embodiments 14-21, wherein the health-associated Propionibacteriumacnes microbe comprises a mixture of two or more different ribotypes.23. The method of any one of embodiments 14-22, wherein thepharmaceutically acceptable excipient or biological stabilizer increasesthe viability of the health-associated Propionibacterium acnes microbeat a temperature from about −10° C. to about 30° C. 25. 24. The methodof any one of embodiments 14-23, wherein the health-associatedPropionibacterium acnes microbe comprises at least one of an HP3A11strain, an HP3B4 strain, an HP4G1, or an HP5G4 strain. 25. The method ofany one of embodiments 14-24, wherein the pharmaceutical probioticcomposition comprises an additional strain of bacteria comprisingPropionibacterium avidum, Propionibacterium acnes subsp. defendens orPropionibacterium granulosum. 26. A pharmaceutical probiotic compositioncomprising: (a) a first therapeutically effective amount of a firsthealth-associated Propionibacterium acnes microbe, wherein the firsthealth-associated Propionibacterium acnes microbe has been engineered orselected to at least one gene encoding at least one of a deoxyriboseoperon repressor and a type II lipase, and less than about 10% pIMPLEplasmid; (b) a second therapeutically effective amount of a secondhealth-associated Propionibacterium acnes microbe, wherein the secondhealth-associated Propionibacterium acnes microbe has been engineered orselected to comprise at least one gene encoding at least one of adeoxyribose operon repressor and a type II lipase, and less than about10% pIMPLE plasmid; and (c) a pharmaceutically acceptable excipient orbiological stabilizer. 27. The pharmaceutical probiotic composition ofembodiment 26, wherein the first or the second health-associatedPropionibacterium acnes microbe has been engineered or selected tocomprise: (i) at least one gene encoding the deoxyribose operonrepressor and the type II lipase, (ii) at least one gene encoding thedeoxyribose operon repressor and less than about 10% pIMPLE plasmid, or(iii) at least one gene encoding the type II lipase and less than about10% pIMPLE plasmid. 28. The pharmaceutical probiotic composition ofembodiment 26 or 27, wherein the first and the second health-associatedPropionibacterium acnes microbe has been engineered or selected tocomprise: (i) at least one gene encoding the deoxyribose operonrepressor and the type II lipase, (ii) at least one gene encoding thedeoxyribose operon repressor and less than about 10% pIMPLE plasmid, or(iii) at least one gene encoding the type II lipase and less than about10% pIMPLE plasmid. 29. The pharmaceutical probiotic composition of anyone of embodiments 26-28, wherein the first or the secondhealth-associated Propionibacterium acnes microbe has been engineered orselected to comprise at least one gene encoding the deoxyribose operonrepressor, the type II lipase, and less than about 10% pIMPLE plasmid.30. The pharmaceutical probiotic composition of any one of embodiments26-29, wherein the first and the second health-associatedPropionibacterium acnes microbe has been engineered or selected tocomprise at least one gene encoding the deoxyribose operon repressor,the type II lipase, and less than about 10% pIMPLE plasmid. 31. Thepharmaceutical probiotic composition of any one of embodiments 26-30,wherein the first and the second health-associated Propionibacteriumacnes microbes are different strains. 32. The pharmaceutical probioticcomposition of any one of embodiments 26-31, wherein the first or thesecond health-associated Propionibacterium acnes microbe comprises anRT1 or RT2 ribotype. 33. The pharmaceutical probiotic composition of anyone of embodiments 26-32, wherein the first health-associatedPropionibacterium acnes microbe comprises an RT1 ribotype and the secondhealth-associated Propionibacterium acnes microbe comprises an RT2ribotype. 34. The pharmaceutical probiotic composition of any one ofembodiments 26-33, wherein neither the first nor the secondhealth-associated Propionibacterium acnes microbe comprises an RT6ribotype. 35. The pharmaceutical probiotic composition of any one ofembodiments 26-34, wherein the pharmaceutically acceptable excipient orbiological stabilizer increases the viability of the health-associated.Propionibacterium acnes microbe at a temperature from about −10° C. toabout −30° C. 36. The pharmaceutical probiotic composition of any one ofembodiments 26-35, for use in the treatment of a skin disorder orcondition. 37. The pharmaceutical probiotic composition of any one ofembodiments 26-36, wherein the health-associated Propionibacterium acnesmicrobe comprise an HP3A11 strain, an HP3B4 strain, an HP4G1 strain, oran HP5G4 strain. 38. The pharmaceutical probiotic composition of any oneof embodiments 26-37, wherein the first or second health-associatedPropionibacterium acnes microbe expresses an ATP binding cassettetransporter. 39. The pharmaceutical probiotic composition of any one ofembodiments 26-38, wherein the first or second health-associatedPropionibacterium acnes microbe does not express a DNA binding responseregulator or a phosphoglycerate kinase. 40. A method of producing adesired preparation of a Propionibacterium acnes bacteria, said methodcomprising: (a) adding a sample of the Propionibacterium acnes bacteriato a glycerol solution to produce a Propionibacterium acnes glycerolstock, and (b) storing the Propionibacterium acnes glycerol stock at atemperature of about 4° C. or less, wherein more than about 50% of theP. acnes bacteria is viable when the Propionibacterium acnes bacteria inthe glycerol solution is brought to ambient temperature. 41. The methodof embodiment 40, wherein the glycerol solution is between about 25% andabout 75% glycerol. 42. The method of embodiment 40 or 41, wherein theglycerol solution is about 50% glycerol. 43. The method of any one ofembodiments 40-42, wherein the temperature is between about 4° C. andabout −80° C. 44. The method of any one of embodiments 40-43, whereinthe temperature is about −20° C. 45. The method of any one ofembodiments 40-44, wherein at least about 70% to at least about 90% ofthe sample is viable after the Propionibacterium acnes glycerol stock isbrought to ambient temperature. 46. The method of any one of embodiments40-45, wherein at least about 90% of the sample is viable after thePropionibacterium acnes glycerol stock is brought to ambienttemperature. 47. The method of embodiment 45 or 46, wherein the ambienttemperature is between about 20° C. and about 30° C. 48. The method ofembodiment 45 or 46, wherein the ambient temperature is about 25° C. 49.The method of any one of embodiments 45-48, wherein thePropionibacterium acnes glycerol stock is brought to ambient temperaturebefore about 90 days of storing. 50. The method of any one ofembodiments 40-49, wherein more than 50% of the sample is viable afterabout 20 days of storing. 51. The method of any one of embodiments40-49, wherein more than about 50% of the sample is viable after about90 days of storing. 52. The method of any one of embodiments 40-49,wherein more than about 50% of the sample is viable at least up to about90 days of storing. 53. The method of any one of embodiments 40-52,wherein Propionibacterium acnes bacteria comprises at least one of anHP3A11 strain, an HP3B4 strain, an HP4G1 strain, or an HP5G4 strain. 54.A method of producing a desired preparation of a preservedPropionibacterium acnes sample, wherein up to about 90% of saidpreserved Propionibacterium acnes sample is viable after sixty days ofstorage, said method comprising: (a) adding a sample ofPropionibacterium acnes bacteria to a solution of between about 1% andabout 50% glycerol in phosphate buffered saline solution to produce aPropionibacterium acnes glycerol stock; and (b) storing thePropionibacterium acnes glycerol stock at a temperature, wherein thetemperature is between about −20° C. and about 30° C., thereby formingsaid desired preparation wherein up to about 90% of said sample ofPropionibacterium acnes bacteria is viable after sixty days of storage.55. A method of producing a desired preparation of a preservedPropionibacterium acnes sample, wherein up to about 90% of saidpreserved Propionibacterium acnes sample is viable after ninety days ofstorage, said method comprising: (a) adding a sample ofPropionibacterium acnes bacteria to a solution of about 50% glycerol toproduce a Propionibacterium acnes glycerol stock; and (b) freezing thePropionibacterium acnes glycerol stock at −20° C., thereby forming saiddesired preparation wherein up to about 90% of said sample ofPropionibacterium acnes bacteria is viable after a thawing of thePropionibacterium acnes glycerol stock. 56. The method of embodiment 55,comprising thawing the Propionibacterium acnes glycerol stock at roomtemperature. 57. The method of embodiment 55 or 56, wherein the solutionis about 1-50% glycerol v/v. 58. The method of any one of embodiments55-57, wherein the solution is about 5-25% glycerol v/v. 59. The methodof any one of embodiments 55-58, wherein the solution is a bufferedsolution. 60. The method of embodiment 59, wherein the buffered solutionis selected from a phosphate buffered saline solution and an acetatebuffered solution. 61. The method of any one of embodiments 55-60,wherein the solution comprises potassium. 62. The method of embodiment61, wherein the solution comprises potassium at a concentration of about150 mM to about 200 mM. 63. The method of any one of embodiments 55-62,wherein the solution comprises calcium. 64. The method of embodiment 63,wherein the solution comprises calcium at a concentration of about 0.05mM to about 0.1 mM. 65. The method of any one of embodiments 55-64,wherein the solution comprises a prebiotic stabilizing agent. 66. Themethod of embodiment 65, wherein the prebiotic stabilizing agent isinulin. 67. The method of embodiment 66, wherein inulin is present inthe solution at a concentration of about 0.05% v/v to about 0.2% v/v.68. The method of any one of embodiments 55-67, wherein the solutioncomprises an anti-acne agent. 69. The method of embodiment 68, whereinthe anti-acne agent comprises a retinoid, a vitamin, an antioxidant, aperoxide, an acid, an oil, an alcohol, an extract, an analog thereof, ora combination thereof. 70. The method of embodiment 69, wherein theretinoid comprises tretinoin, tazarotene, adapalene, retinol, or acombination thereof. 71. The method of embodiment 69, wherein thevitamin or analog thereof comprises Vitamin D, Vitamin C, Vitamin E, orcalciptotriene. 72. The method of embodiment 69, wherein the antioxidantcomprises Vitamin C or Vitamin E. 73. The method of embodiment 69,wherein the peroxide is benzoyl peroxide. 74. The method of embodiment69, wherein the acid comprises salicylic acid, azaelic acid,trichloracetic acid, or glycolic acid. 75. The method of embodiment 69,wherein the alcohol comprises retinol or resveratrol. 76. The method ofembodiment 69, wherein the oil is tea tree oil. 77. The method ofembodiment 69, wherein the extract is a green tea extract. 78. Themethod of any one of embodiments 54-77, wherein the solution isincorporated in a biologic stability platform to eliminate cold chainstorage. 79. The method of embodiment 78, wherein the biologic storageplatform comprises foam drying or foam formation of the solution orglycerol stock solution. 80. The method of embodiment 78, wherein thesolution comprises at least one of a glyconanoparticle, a liposome, ananoparticle, trehalose, sucrose, stachyose, hydroxyethyl starch, or acombination of glycine and mannitol. 81. The method of any one ofembodiments 54-80, wherein the sample of Propionibacterium acnesbacteria comprises Propionibacterium acnes bacteria of ribotype RT1. 82.The method of any one of embodiments 54-80, wherein the sample ofPropionibacterium acnes bacteria comprises Propionibacterium acnesbacteria of ribotype RT2. 83. The method of any one of embodiments54-80, wherein the sample of Propionibacterium acnes bacteria comprisesPropionibacterium acnes bacteria of ribotype RT1 and RT2. 84. The methodof any one of embodiments 54-83, wherein the Propionibacterium acnesbacteria is characterized by at least one of the following: comprises adeoR protein; comprises a type II lipase; comprises less than 10% pIMPLEplasmid; does not comprise a Cas5 protein; comprises an ATP bindingcassette transporter protein; does not comprise a DNA binding responseregulator; and does not comprise a phosphoglycerate kinase. 85. Themethod of any one of embodiments 54-83, wherein the sample ofPropionibacterium acnes bacteria comprises Propionibacterium acnesbacteria comprises an HP3A11 strain, an HP3B4 strain, an HP4G1 strain,an HP5G4 strain. 86. A pharmaceutical composition comprising: (a) atherapeutically effective amount of a health-associatedPropionibacterium acnes microbe, wherein the health-associatedPropionibacterium acnes microbe is characterized by at least one of thefollowing: comprises at least one gene encoding at least one of adeoxyribose operon repressor and a type II lipase, and less than about10% pIMPLE plasmid; comprises at least one gene encoding an ATP bindingcassette transporter; or lacks at least one gene encoding a DNA bindingresponse regulator or a phosphoglycerate kinase, and (b) apharmaceutically acceptable excipient or biological stabilizer. 87. Thepharmaceutical probiotic composition of embodiment 86, wherein thehealth-associated Propionibacterium acnes microbe has been engineered orselected to comprise a deoxyribose operon repressor and a type IIlipase. 88. The pharmaceutical probiotic composition of embodiment 86 or87, wherein a Cas5 protein is absent from the health-associatedPropionibacterium acnes microbe. 89. The pharmaceutical probioticcomposition of any one of embodiments 86-88, wherein thehealth-associated Propionibacterium acnes microbe expresses an ATPbinding cassette transporter. 90. The pharmaceutical probioticcomposition of any one of embodiments 86-89, wherein thehealth-associated Propionibacterium acnes microbe does not express a DNAbinding response regulator or a phosphoglycerate kinase. 91. Thepharmaceutical probiotic composition of any one of embodiments 86-90,wherein the health-associated Propionibacterium acnes microbe comprisesan RT1 or RT2 ribotype. 92. The pharmaceutical probiotic composition ofany one of embodiments 86-91, wherein the health-associatedPropionibacterium acnes microbe does not comprise an RT6 ribotype. 93.The pharmaceutical probiotic composition of any one of embodiments86-92, wherein the health-associated Propionibacterium acnes microbecomprises less than about 1% pIMPLE plasmid. 94. The pharmaceuticalprobiotic composition of any one of embodiments 86-93, wherein thehealth-associated Propionibacterium acnes microbe comprises less thanabout 0.3% pIMPLE plasmid. 95. The pharmaceutical probiotic compositionof any one of embodiments 86-94, wherein the pharmaceutically acceptableexcipient or biological stabilizer increases the viability of thehealth-associated Propionibacterium acnes microbe at a temperature fromabout −20° C. to about 30° C. 96. The pharmaceutical composition of anyone of embodiments 86-95, wherein the health-associatedPropionibacterium acnes microbe comprises a mixture of two or moredifferent ribotypes of Propionibacterium acnes. 97. The pharmaceuticalprobiotic composition of any one of embodiments 86-96, wherein thehealth-associated Propionibacterium acnes microbe comprises an HP3A11strain, an HP3B4 strain, an HP4G1 strain, or an HP5G4 strain. 98. Thepharmaceutical probiotic composition of any one of embodiments 86-97,comprising an additional strain of bacteria, wherein the additionalstrain comprises Propionibacterium avidum, Propionibacterium acnessubsp. defendens, or Propionibacterium granulosum. 99. A method oftreating a skin disorder or condition comprising applying atherapeutically effective amount of a pharmaceutical probioticcomposition comprising: (a) a therapeutically effective amount of ahealth-associated Propionibacterium acnes microbe, wherein thehealth-associated Propionibacterium acnes microbe is characterized by atleast one of the following: comprises at least one gene encoding atleast one of a deoxyribose operon repressor and a type II lipase, andless than about 10% pIMPLE plasmid; comprises at least one gene encodingan ATP binding cassette transporter; or lacks at least one gene encodinga DNA binding response regulator or a phosphoglycerate kinase, and (b) apharmaceutically acceptable excipient or biological stabilizer. 100. Themethod of embodiment 99, wherein the skin disorder or conditioncomprises acne, eczema, seborrheic dermatitis, psoriasis, or rosacea, ora combination thereof. 101. The method of embodiment 99 or 100, whereinthe health-associated Propionibacterium acnes microbe has beenengineered or selected to at least one gene encoding the deoxyriboseoperon repressor and the type II lipase. 102. The method of any one ofembodiments 99 to 101, wherein a Cas5 protein is absent from thehealth-associated Propionibacterium acnes microbe. 103. The method ofany one of embodiments 99 to 102, wherein the health-associatedPropionibacterium acnes microbe comprises an RT1 or RT2 ribotype. 104.The method of any one of embodiments 99 to 103, wherein thehealth-associated Propionibacterium acnes microbe does not comprise anRT6 ribotype. 105. The method of any one of embodiments 99 to 104,wherein the health-associated Propionibacterium acnes microbe comprisesless than about 1% pIMPLE plasmid. 106. The method of any one ofembodiments 99 to 105, wherein the health-associated Propionibacteriumacnes microbe comprises less than about 0.3% pIMPLE plasmid. 107. Themethod of any one of embodiments 99 to 106, wherein the pharmaceuticallyacceptable excipient or biological stabilizer increases the viability ofthe health-associated Propionibacterium acnes microbe at a temperaturefrom about −20° C. to about 30° C. 108. The method of any one ofembodiments 99 to 107, wherein the health-associated Propionibacteriumacnes microbe comprises a mixture of two or more different ribotypes.109. The method of any one of embodiments 99 to 108, wherein thehealth-associated Propionibacterium acnes microbe comprises an HP3A11strain, an HP3B4 strain, an HP4G1 strain, or an HP5G4 strain. 110. Themethod of any one of embodiments 99 to 109, wherein the pharmaceuticalprobiotic composition comprises an additional strain of bacteria,wherein the additional strain comprises Propionibacterium avidum,Propionibacterium acnes subsp. defendens, or Propionibacteriumgranulosum. 111. A pharmaceutical probiotic composition comprising: (a)a first therapeutically effective amount of a first health-associatedPropionibacterium acnes microbe, wherein the first health-associatedPropionibacterium acnes microbe is characterized by at least one of thefollowing: comprises at least one gene encoding at least one of adeoxyribose operon repressor and a type II lipase, and less than about10% pIMPLE plasmid; comprises at least one gene encoding an ATP bindingcassette transporter; or lacks at least one gene encoding a DNA bindingresponse regulator or a phosphoglycerate kinase; (b) a secondtherapeutically effective amount of a second health-associated microbe;and (c) a pharmaceutically acceptable excipient or biologicalstabilizer. 112. The pharmaceutical probiotic composition of embodiment111, wherein the second health-associated microbe is a strain ofbacteria comprising P. acnes, P. granulosum, P. acnes subsp. defendensor P. avidum. 113. The pharmaceutical probiotic composition of claim 111or 112, wherein the second health-associated microbe is characterized byat least one of the following: comprises at least one gene encoding atleast one of a deoxyribose operon repressor and a type II lipase, andless than about 10% pIMPLE plasmid; comprises at least one gene encodingan ATP binding cassette transporter; or lacks at least one gene encodinga DNA binding response regulator or a phosphoglycerate kinase. 114. Thepharmaceutical probiotic composition of any one of embodiments 111-113,wherein the second health-associated microbe is a strain of P. acnesbacteria of ribotype RT1 or RT2. 115. The pharmaceutical probioticcomposition of any one of embodiments 111-114, wherein the firsthealth-associated Propionibacterium acnes microbe or the secondhealth-associated microbe comprises an isolated or purified strain ofbacteria. 116. A pharmaceutical composition comprising: (a) apharmaceutically acceptable excipient or biological stabilizer; and (b)a therapeutically effective amount of a health-associatedPropionibacterium acnes microbe, wherein the health-associatedPropionibacterium acnes microbe does not express a DNA binding responseregulator, a phosphoglycerate kinase, or a combination thereof. 117. Apharmaceutical composition comprising: (a) a pharmaceutically acceptableexcipient or biological stabilizer; and (b) a therapeutically effectiveamount of a health-associated Propionibacterium acnes microbe, whereinthe health-associated Propionibacterium acnes microbe expresses anATP-binding cassette transporter. 118. A pharmaceutical compositioncomprising: (a) a pharmaceutically acceptable excipient or biologicalstabilizer; and (b) a therapeutically effective amount of ahealth-associated Propionibacterium acnes microbe, wherein thehealth-associated Propionibacterium acnes microbe: does not express aDNA binding response regulator, a phosphoglycerate kinase, or acombination thereof; and expresses an ATP-binding cassette transporter.119. The pharmaceutical of any one of embodiments 86, 116, and 118,wherein the DNA binding response regulator is encoded by a sequence ofSEQ ID NO: 7. 120. The pharmaceutical of any one of embodiments 86, 116,and 118, wherein the DNA binding response regulator is encoded by asequence that is at least 50% homologous to a sequence of SEQ ID NO: 7.121. The pharmaceutical of any one of embodiments 86, 116, and 118,wherein the phosphoglycerate kinase is encoded by a sequence of SEQ IDNO: 9. 122. The pharmaceutical of any one of embodiments 86, 116, and118, wherein the phosphoglycerate kinase is encoded by a sequence thatis at least 50% homologous to a sequence of SEQ ID NO: 9. 123. Thepharmaceutical of embodiment 116 or 117, wherein the ATP-bindingcassette transporter is encoded by a sequence of SEQ ID NO: 6. 124. Thepharmaceutical of any one of embodiments 86, 117, and 118, wherein theATP-binding cassette transporter is encoded by a sequence that is atleast 50% homologous to a sequence of SEQ ID NO: 6. 125. Thepharmaceutical composition of any one of embodiments 86 and 116-124,comprising at least two strains of bacteria. 126. The pharmaceuticalcomposition of any one of embodiments 86 and 116-125, comprising astrain of Propionibacterium acnes having a ribotype of RT1, RT2, RT3,RT4 or RT5. 127. The pharmaceutical composition of any one ofembodiments 86 and 116-126, comprising a strain of Propionibacteriumacnes having a ribotype of RT1 or RT2. 128. The pharmaceutical probioticcomposition of any one of embodiments 86 and 116-127, wherein thehealth-associated Propionibacterium acnes microbe does not comprise anRT6 ribotype. 129. The pharmaceutical composition of any one ofembodiments 86 and 116-128, wherein the pharmaceutical composition isformulated for topical administration. 130. The pharmaceuticalcomposition of any one of embodiments 86 and 116-129, wherein thepharmaceutical composition is in the form of a gel, ointment, lotion,emulsion, paste, cream, foam, mousse, liquid, spray, suspension,dispersion and aerosol. 131. The pharmaceutical composition of any oneof embodiments 86 and 116-130, comprising a liposome or nanoparticle.132. The pharmaceutical probiotic composition of any one of embodiments86 and 116-131, wherein the health-associated Propionibacterium acnesmicrobe comprises a deoxyribose operon repressor and a type II lipase.133. The pharmaceutical probiotic composition of any one of embodiments86 and 116-132, wherein a Cas5 protein is absent from thehealth-associated Propionibacterium acnes microbe. 134. Thepharmaceutical probiotic composition of any one of embodiments 86 and116-133, wherein the health-associated Propionibacterium acnes microbecomprises less than about 1% pIMPLE plasmid. 135. The pharmaceuticalprobiotic composition of any one of embodiments 86 and 116-133, whereinthe health-associated Propionibacterium acnes microbe comprises lessthan about 0.3% pIMPLE plasmid. 136. The pharmaceutical composition ofclaim of any one of embodiments 86 and 116-135, wherein thehealth-associated Propionibacterium acnes microbe comprises a mixture oftwo or more different ribotypes of Propionibacterium acnes. 137. Thepharmaceutical probiotic composition of any one of embodiments 86 and116-136, wherein the pharmaceutically acceptable excipient or biologicalstabilizer increases the viability of the health-associatedPropionibacterium acnes microbe at a temperature from about −10° C. toabout 30° C. 138. The pharmaceutical probiotic composition of any one ofembodiments 86 and 116-137, comprising an additional strain of bacteria.139. The pharmaceutical probiotic composition of any one of embodiments86 and 116-137, comprising an additional strain of bacteria, wherein theadditional strain comprises Propionibacterium avidum, Propionibacteriumacnes subsp. defendens or Propionibacterium granulosum. 140. Thepharmaceutical probiotic composition of any one of embodiments 86 and116-137, wherein the health-associated Propionibacterium acnes microbeis selected, transformed or engineered to: comprise at least one geneencoding at least one of a deoxyribose operon repressor and a type IIlipase, and less than about 10% pIMPLE plasmid; comprise at least onegene encoding an ATP binding cassette transporter; or lack at least onegene encoding a DNA binding response regulator or a phosphoglyceratekinase. 141. A method of treating a skin disorder or conditioncomprising applying a therapeutically effective amount of apharmaceutical composition of any one of embodiments 86 and 116-140.142. The method of embodiment 141, wherein the skin disorder orcondition comprises acne, eczema, seborrheic dermatitis, psoriasis, orrosacea, or a combination thereof 143. A pharmaceutical compositioncomprising: (a) a first therapeutically effective amount of a firsthealth-associated Propionibacterium microbe, wherein the firsthealth-associated Propionibacterium microbe produces less than about onemicromolar porphyrin; (b) a second therapeutically effective amount of asecond health-associated microbe; and (c) a pharmaceutically acceptableexcipient or biological stabilizer. 144. The pharmaceutical compositionof embodiment 143, wherein the second health-associated microbecomprises a strain of Propionibacterium. 145. The pharmaceuticalcomposition of embodiment 143 or 144, wherein, wherein the secondhealth-associated microbe produces less than about one micromolarporphyrin. 146. The pharmaceutical composition of any one of embodiments143-145, wherein the first health-associated Propionibacterium microbeand the second health-associated Propionibacterium microbe collectivelyproduce less than about one micromolar porphyrin. 147. Thepharmaceutical composition of any one of embodiments 143-146, wherein atleast one of the first health-associated Propionibacterium microbe andthe second health-associated Propionibacterium microbe produce less thanabout 200 nM porphyrin. 148. The pharmaceutical composition of any oneof embodiments 143-146, wherein at least one of the firsthealth-associated Propionibacterium microbe and the secondhealth-associated Propionibacterium microbe produce less than about 100nM porphyrin. 149. The pharmaceutical composition of any one ofembodiments 143-148, wherein the first health-associatedPropionibacterium microbe and the second health-associatedPropionibacterium microbe collectively produce less than about 100 nMporphyrin. 150. The pharmaceutical composition of any one of embodiments143-149, wherein at least one of the first health-associatedPropionibacterium microbe and the second health-associatedPropionibacterium microbe produce less than about one micromolarporphyrin in situ. 151. The pharmaceutical composition of any one ofembodiments 143-150, wherein at least one of the first health-associatedPropionibacterium microbe and the second health-associatedPropionibacterium microbe produce less than about one micromolarporphyrin in vitro. 152. The pharmaceutical composition of any one ofembodiments 143-151, wherein at least the first health-associatedPropionibacterium microbe comprises a strain of Propionibacterium acnes,Propionibacterium granulosum, Propionibacterium avidum, orPropionibacterium acnes subsp. defendens. 153. The pharmaceuticalcomposition of any one of embodiments 143-152, wherein at least thefirst health-associated Propionibacterium microbe comprises a strain ofPropionibacterium acnes. 154. The pharmaceutical composition of any oneof embodiments 143-153, wherein at least the first health-associatedPropionibacterium microbe comprises a Propionibacterium acnes of aribotype RT1 or RT2. 155. The pharmaceutical composition of any one ofembodiments 143-154, wherein at least the first health-associatedPropionibacterium microbe: (a) comprises at least one gene encoding anATP binding cassette transporter; (b) comprises at least one geneencoding at least one of a deoxyribose operon repressor and a type IIlipase, and less than about 10% pIMPLE plasmid; or (c) lacks at leastone gene encoding a DNA binding response regulator or a phosphoglyceratekinase.

EXAMPLES

The following examples are given for the purpose of illustrating variousembodiments of the disclosure and are not meant to limit the presentdisclosure in any fashion. The present examples, along with the methodsdescribed herein are presently representative of preferred embodiments,are exemplary, and are not intended as limitations on the scope of thedisclosure. Changes therein and other uses which are encompassed withinthe spirit of the disclosure as defined by the scope of the claims willoccur to those skilled in the art.

Example 1: Identification of Health-Associated Strains

Characteristics that may predispose a particular microbe to be ahealth-associated microbe can be determined using samples from healthyand disease afflicted individuals, culturing the microbes from each, andperforming a comparative genomic analysis. In the present example,samples were collected from individuals afflicted with acne vulgaris inorder to determine health-associated P. acnes strains.

Microcomedone or swab samples were collected from consented adultsubjects. Clonal samples were isolated by limiting dilution on plates,and then grown in 200 μL of liquid culture. Microbial DNA was isolatedfrom 96 individual cultures. DNA was isolated using QlAgen's DNeasyBlood & Tissue kit, following the manufacturer's instructions. QIAgen'sDNeasy Blood & Tissue kit, following the manufacturer's instructions.Paired-end DNA sequencing (2×300 bp) was done on an Illumina MiSeq usingreagent kit v3, following the manufacturer's instructions, yielding200,000 to 600,000 reads for each of the 96 samples. Initial analysiswas performed in Illumina's Basespace Sequence Hub, all reads from eachsample are aligned with a BWA Aligner to:

a. deoR;

b. Propionibacterium acnes ATCC 11828 (accession CP003084); or

c. pIMPLE and other reference genomes.

Alignments were interrogated with the Broad Institute's IntegrativeGenomics Viewer and confirmed using Biomatter's Geneious version 9.1.All 96 clones were analyzed for the presence or absence of the deoRsequence, type I lipase or type II lipase sequence, and presence orabsence of pIMPLE plasmid. Sequence alignments were performed betweensequences of P. Acnes from healthy volunteers and the deoR gene.Analysis revealed that approximately half of all healthy clones werepositive for deoR (greater than 0.4% of reads mapping to deoR locus).Sequence alignments were also performed between P. acnes of healthyvolunteers and the lipase gene locus P. acnes were positive for type ILipase and for type II Lipase. With regard to the pIMPLE plasmidsequence alignments of reads from healthy volunteers performed againstpIMPLE-HL096PA1 (GenBank: CP003294.1), revealed P. acnes from healthyvolunteers are free of pIMPLE plasmid. Reads from healthy volunteers mapP. acnes to ribotype RT1. FIG. 2 corroborates this by showing that moreRT1 strains are deoR positive and type II lipase positive when compareto RT2. Some results are summarized in Table 2.

TABLE 2 summary of sequencing data for the P. acnes isolated fromhealthy volunteers RT1; RT1; RT1; deoR+; deoR+; deoR− LP1 LP2 RT2 Staph.Other sum reads 112 160 42 1 7 48 370 % of total 30.3% 43.2% 11.4% 0.3%1.9% 13.0% RT1 = ribotype 1; RT2 = ribotype 2; deoR− = no deoR; deoR+ =deoR; LP1 = type I; Lipase; PL2 = type II lipase; Staph =Staphylococcus; other P. avidum, P. acidipropionici, or Staphylococcus

Example 2: Identification of Health-Associated Strains withHyaluronidase Genes

Health-associated P. acnes clones that were RT1 or RT2 positive werefurther examined for presence of a gene encoding hyaluronidase.Unexpectedly most health-associated strains that were positive for TypeII lipase also possessed a hyaluronidase gene. See Table 3.

TABLE 3 Hyaluronidase presence in health-associated P. acnes strainsalso positive for type II lipase Clone Ribotype Hyaluronidase 1 RT1;deoR+; L2 Yes 2 RT1; deoR+; L2 Yes 3 RT1; deoR+; L2 Yes 4 RT1; deoR+; L2Yes 5 RT1; deoR+; L2 Yes 6 RT1; deoR+; L1 No 7 RT1; deoR+; L2 Yes 8 RT1;deoR+; L2 Yes 9 RT1; deoR+; L2 Yes 10 RT1; deoR+; L2 Yes 11 RT1; deoR+;L2 Yes 12 RT2 Yes 13 RT2 Yes 14 RT2 Yes 15 RT2 Yes RT1 = Ribotype 1; RT2= Ribotype 2; L1—Lipase type I; L2 = Lipase type 2; Deor+ = DeoRepressorpositive

Example 3: P. Acnes Viability Assay

Viability of P. acnes was assessed each week over two months of storageas shown in Table 4. At least three samples were tested at each timepoint.

TABLE 4 Assessed P. acnes storage conditions Solution Temperature 25%glycerol in water  4° C. 50% glycerol in water  4° C. 25% glycerol in75% PBS  4° C. 25% glycerol in water −20° C. 50% glycerol in water −20°C. 25% glycerol in water −80° C.

Samples were prepared according to the following:

1. P. acnes of ribotypes RT1 (HP3A11) and RT2 (HP5G4) were started at0.066 OD600 and grown to ˜1.0 OD600 in exponential phase in reinforcedclostridial medium (RCM).

2. A day later, cultures displayed a dense turbidity, and they weresplit 1:2 with RCM to produce four liquid culture (LC) samples of eachribotype: 4 RT2 LC and 4 RT1 LC.

3. Two days later, resulting pellets and media were separated. The mediaof the LC was split between two tubes (˜3 ml), and tubes were filledwith 9 ml fresh media and vortexed. Pellets remained in original testtubes and were resuspended by pipetting with 8 ml fresh RCM. All LC (the8 pellet LCs (4 RT1 and 4RT2), and 16 media-derived LCs) were placedinto a jar with two sachets given a large quantity of oxygen filled thejar.

4. LCs were vortexed, split and fed fresh media as they became veryturbid and large pellets formed.

5. A day before the experiment, cultures were vortexed, split, spun downat 4,300 g for 5 minutes, and media replaced.

6. On the day of initiating storage: LCs were split into sterile 50 mlconical tube (e.g., 50 ml aliquots of RT1 or RT2), avoiding the pelletedcells. Conical tubes were vortexed lightly and OD600 measured.Optionally, LCs may be diluted if OD600 is greater than 1.0.

7. LCs were split into aliquots and spun down at 4,000 rcf for 5minutes. Media was discarded and pellets washed with 5 ml 25% v/vglycerol/water to wash the cells. Cells were centrifuged once more, andwash solution discarded.

8. Cells were added to 8.75 ml 25% glycerol in water, 6 ml 50% glycerolin water or 3.25 ml 25% glycerol in PBS to produce live bacteriasolutions.

9. 250 microliters of live bacteria solutions were added to 1.5 mleppendorf tubes, and placed at 4° C., −20° C. or −80° C.

Cell viability was assessed according to the following:

1. At each time point, Eppendorf tubes were selected from eachtreatment, and allowed to come to room temperature. Tubes were invertedsix times.

2. 20 microliters of the thawed stocks were serially diluted in 96 wellplates with RCM.

3. Thawed stocks were also spotted on Brucella plates at variousdilutions.

4. Plates were imaged with a digital camera, and cells counted with 95%Confidence Interval.

FIG. 3 shows the viability of a variety of Ribotype 1 and Ribotype 2 P.acnes preparations after 30 days, 60 days and 90 days of preservation.Heat shock of a sample, simulating direct application to skin,demonstrated that these samples would retain reported viability if usedfor acne treatment.

Example 4. Identification of P. acnes RT6

In an effort to isolate and purify health-associated strains of P.acnes, (e.g., strains associated with acne) it may be useful to identifyundesirable strains of P. acnes in a sample (e.g., strains found on skinof subjects with acne). For instance, in some cases, P. acnes ofribotype RT6 is undesirable. To this end, genes can be identified thatare specific to strains of interest. The following example demonstrateshow this can be performed.

Identities of genes that distinguish P. acnes of ribotype RT6 fromhealthy strains were confirmed. Genes encoding DNA binding responseregulator and phosphoglycerate kinase were identified in P. acnes ofribotype RT6, but not RT1, RT2, RT3, RT4 and RT5. In addition a geneencoding ABC transporter is absent in RT6, but present in RT1, RT2, RT3,RT4 and RT5. Sequences for these genes are provided as SEQ ID NOS: 6(ABC transporter), 7 (DNA binding response regulator), and 9(phosphoglycerate kinase)

The presence or absence of these genes was confirmed by sequencealignment using BLAST, Megablast, (a registered trademark of theNational Library of Medicine) either the whole complete genome or all ofthe scaffolds of a completed genome against each of these three genesequences; the results are shown in Table 5. “Y” is a perfect match forthe entire sequence OR>60 bp continuous perfect sequence alignment. “N”means there is <60 bp perfect alignment. The best match of a “N” was 26bp.

TABLE 5 Characterization of exemplary P. acnes strains DNA ABC bindingrecA trans- response Phosphoglycerate Strain Name Ribotype type porterregulator kinase HL002PA2 1 IA Y N N HL025PA1 1 IB Y N N HL030PA1 1 IB YN N HL050PA2 1 II Y N N HL096PA3 1 IA Y N N HP3A11 1 IB Y N N HP3B4 1 YN N KPA171202 1 IB Y N N ATCC 11828 2 II Y N N HL001PA1 2 II Y N NHL103PA1 2 II Y N N HP4G1 2 II Y N N HP5G4 2 II Y N N HL002PA1 3 IB Y NN HL005PA1 4 IA Y N N HL007PA1 4 IA Y N N HL038PA1 4 IA Y N N HL045PA1 4IA Y N N HL053PA1 4 IA Y N N HL056PA1 4 IA Y N N HL074PA1 4 IA Y N NHL099PA1 4 IA Y N N HL043PA1 5 IA Y N N HL043PA2 5 IA Y N N HL072PA1 5IA Y N N HL072PA2 5 IA Y N N HL096PA1 5 IA Y N N HL096PA2 5 IA Y N NHL097PA1 5 IC Y N N PRP-38 5 IC Y N N HL110PA3 6 II N Y Y HL110PA4 6 IIN Y Y

Example 5. Pan Bacterial Assay to Characterize Skin Microbiome

Robust pan-sampling of the skin microbiome is demonstrated in thefollowing example. This can be performed with or without the use ofpreservatives. This method is compatible with qPCR analysis and does notrequire DNA purification. TaqMan qPCR assays were used to quantitatemost bacteria collected from the face. Performance was confirmed withtwo different bacterial phyla, all Propionibacterium and Staphylococcus.This method required the assessment of only a single locus to recognizemost bacteria commonly found on the face (P. acnes strains andStaphylococcus), whereas current methods in the field use multipleprimer pairs to achieve similar coverage. The majority of the bacteriaon the skin of a subject's face is described in the following Table 6.

TABLE 6 Bacteria on Human Facial Skin P. acnes P. avidum S. epidermidisS. aureus Kingdom Bacteria Bacteria Bacteria Bacteria PhylumActinobacteria Actinobacteria Firmicutes Firmicutes Bacilli BacilliOrder Actinomycetales Actinomycetales Bacillales Bacillales FamilyPropionibacteriaceae Propionibacteriaceae StaphylococcaceaeStaphylococcaceae Genus Propionibacterium PropionibacteriumStaphylococcus Staphylococcus Species P. acnes P. avidum S. epidermidisS. aureus

A portion of a 23S sequence from bacteria commonly found on the humanface was aligned with known sequences, see FIG. 4, and SEQ ID NOs: 33 to43. Despite two Single Nucleotide Polymorphisms at this loci (denoted bybold and underlined letters), careful placement of primers (gray andblack) and TaqMan reporter (white) enable quantification of widelydiverse bacteria from both Actinobacteria and Firmicutes.

A standard curve for all assays was generated with P. acnes. Percentagesof health-associated P. acnes were computed using a dilution series withS. epidermidis or pathogenic P. acnes which were used to quantitate apercentage of health-associated P. acnes in a collected sample. Thesepercentages were determined by measuring deoR+ or Cas5+ bacteria in theoverall sample of bacteria (PANBAC), see, e.g., FIG. 5.

Example 6. Determination of Percentage of pIMPLE Plasmid

The percentage of pIMPLE plasmid was determined from biological samples.

Biological samples were collected and grown in 200 μL of liquid culture.DNA was isolated using QlAgen's DNeasy Blood & Tissue kit, following themanufacturer's instructions. Paired-end DNA sequencing (2×300 bp) wasdone on an Illumina MiSeq using reagent kit v3, following themanufacturer's instructions, yielding 200,000 to 600,000 reads for eachsample. Initial analysis was performed in Illumina's Basespace SequenceHub, all reads from each sample are aligned with a BWA Aligner topIMPLE. Alignments were interrogated with the Broad Institute'sIntegrative Genomics Viewer and confirmed using Biomatter's Geneiousversion 9.1.

The percentage of pIMPLE was determined by the percentage of totalsequencing reads that aligned to pIMPLE plasmid from HL096PA1. Thepercentage of pIMPLE was also calculated as the coverage*copy number.Using these methods, the percentage of pIMPLE in the different ribotypeswas determined as seen in Table 7.

TABLE 7 Presence of pIMPLE plasmid in different P. acnes strains.Ribotype Strain % pIMPLE 1 HP3A11 0.23% 1 HP3A11 0.24% 2 HP5G4 0.26% 2HP5G4 0.24% 2 HP4G1 0.26% 2 HP4G1 0.25% 4 HL045PA1 3.62% 4 HL045PA13.22% 5 HL043PA1 4.32% 5 HL043PA1 3.75% 6 HL110PA3 12.94% 6 HL110PA312.59% 6 HL110PA4 13.19% 6 HL110PA4 14.06%

Example 7. Genetic Modification of P. Acnes

In order to improve healthy P. acnes clones, the expression of a gene inthe porphyrin synthetic pathway was knocked out. This was accomplishedby inserting stop codons in the middle of the open reading frame of thegene HemY (protoporphyrinogen oxidase, EC:1.3.3.4 1.3.3.15) in the P.acnes genome. Briefly, the RNA-guided DNA endonuclease Cas9 (CRISPRassociated protein 9) was targeted to HemY with specific CRISPR RNA(crRNA), and trans-activating RNA (tracrRNA) cleaving a double strandedbreak at the desired location in the HemY gene. A specific sequence wasinserted at the site of the cleavage with a Homology Directed Repaircassette (HDR).

The Cas9, crRNA, tracrRNA, and HDR donor template were introduced intoP. acnes using electroporation to transform the cells. Cells must beelectrocompetent before undergoing electroporation. Electrocompetent P.acnes were prepared by growing them to stationary phase and washing themin a buffer of sucrose, magnesium chloride, and monosodium phosphate.

The tracrRNA and crRNA were duplexed using IDT's duplex-forming buffer.Then the tracrRNA:crRNA duplex was incubated in a solution of Cas9 andphosphate-buffered saline, forming the ribonucleoprotein (RNP) complex.The RNPs, HDR, and electrocompetent P. acnes were combined, incubated onice (transformation culture) and transferred to a pre-chilled BioRADelectroporation cuvette. The transformation culture was electroporatedusing a BioRAD Micropulser. Rich clostridium medium was immediatelyadded to the transformation culture and transferred to separatecontainer for a 24 hour, room temperature incubation. The transformationculture was evaluated with qPCR (see FIG. 6) and spread out overmultiple Brucella plates for a final 72 hour anaerobic incubation at 37°C.

FIG. 6 compares a qPCR result from cells transformed with a 921 bp (921)or a 123 bp HDR. Each sample was evaluated with primers that recognizedeither the inserted sequence (Insert) or the untransformed or wild-type(wt) genomic sequence. Note, using the longer, 921 bp, HDR transformed agreater percentage of the cells. The ‘921’ sample had more cellsresulting the leftward shift of both Insert and wt lines.

Example 8. Packaging Compositions of Bacteria as Swabs for TopicalApplication

A packaging system was created to store and deliver therapeuticallyeffective doses of pharmaceutical probiotic compositions disclosedherein to the human face. These devices need to safely store and deliverapproximately 4 milliliters of P. acnes in a pharmaceutically acceptableexcipient, anaerobically. Furthermore, these systems were amenable tostorage at temperatures as low as −80° C. The packaging system preventedcontamination of both the probiotic (by the environment) and theenvironment (by the probiotic), minimize exposure to any air, and enableeasy application.

An example of an aforementioned package is shown in FIG. 8. Briefly anapproximately 2 inch diameter circular cotton pad was placed in alaminated polypropylene bag. Three to five milliliters of P. acnessolution, at −10⁹ microbes per milliliter, was aseptically applied tothe cotton pad. Almost all of the air was evacuated, and the bag wasthermally sealed in a chamber vacuum sealer (Vacmaster VP215). Thesepackages were easily opened and the pad removed for application of theprobiotic or measurement of recovery and viability. Near quantitativeaseptic recovery was achieved by centrifugation of the pad in a 15milliliter conical tube. To confirm that the cotton pad, polypropylenebags and high vacuum do not compromise viability of P. acnes, or retainP. acnes, samples were collected from four different conditions anddetermined CFUs/milliliter by plating and counting colonies. FIG. 9compares recovery from P. acnes samples stored for one week at −20° C.in either an Eppendorf tube (control), or in our packaging in aresidential frost free freezer, a laboratory freezer or in the labfreezer with only a light vacuum before sealing. Large numbers of viableP. acnes were recovered from all conditions.

Alternative types of pads and bags could be employed for such packaging.For example, if a polyester pad is used, heat sealing could affix thepad to one side of the bag providing a shield and handle to enableapplication of the liquid therapeutic without mess and exposure to thehand. Similarly if a peel-open pouch is used, scissors would not benecessary for clean easy application.

While preferred embodiments of the present invention have been shown anddescribed herein, it will be obvious to those skilled in the art thatsuch embodiments are provided by way of example only. Numerousvariations, changes, and substitutions will now occur to those skilledin the art without departing from the invention. It should be understoodthat various alternatives to the embodiments of the invention describedherein may be employed in practicing the invention.

1. A pharmaceutical composition comprising: a) a therapeuticallyeffective amount of a health-associated Propionibacterium acnes microbe,wherein the health-associated Propionibacterium acnes microbe ischaracterized by at least one of the following: i) comprises at leastone gene encoding at least one of a deoxyribose operon repressor and atype II lipase, and less than about 10% pIMPLE plasmid; ii) comprises atleast one gene encoding an ATP binding cassette transporter; or iii)lacks at least one gene encoding a DNA binding response regulator or aphosphoglycerate kinase, and b) a pharmaceutically acceptable excipientor biological stabilizer.
 2. The pharmaceutical probiotic composition ofclaim 1, wherein the health-associated Propionibacterium acnes microbehas been engineered or selected to comprise a deoxyribose operonrepressor and a type II lipase.
 3. (canceled)
 4. The pharmaceuticalprobiotic composition of claim 1, wherein the health-associatedPropionibacterium acnes microbe expresses an ATP binding cassettetransporter.
 5. The pharmaceutical probiotic composition of claim 1,wherein the health-associated Propionibacterium acnes microbe does notexpress a DNA binding response regulator or a phosphoglycerate kinase.6. The pharmaceutical probiotic composition of claim 1, wherein thehealth-associated Propionibacterium acnes microbe comprises an RT1 orRT2 ribotype.
 7. The pharmaceutical probiotic composition of claim 1,wherein the health-associated Propionibacterium acnes microbe does notcomprise an RT6 ribotype. 8-10. (canceled)
 11. The pharmaceuticalprobiotic composition of claim 1, wherein the health-associatedPropionibacterium acnes microbe comprises an HP3A11 strain, an HP3B4strain, an HP4G1 strain, or an HP5G4 strain.
 12. The pharmaceuticalprobiotic composition of claim 1, comprising an additional strain ofbacteria, wherein the additional strain comprises Propionibacteriumavidum, Propionibacterium acnes subsp. defendens, or Propionibacteriumgranulosum.
 13. A method of treating a skin disorder or conditioncomprising applying a therapeutically effective amount of apharmaceutical probiotic composition comprising: a. a therapeuticallyeffective amount of a health-associated Propionibacterium acnes microbe,wherein the health-associated Propionibacterium acnes microbe ischaracterized by at least one of the following: i) comprises at leastone gene encoding at least one of a deoxyribose operon repressor and atype II lipase, and less than about 10% pIMPLE plasmid; ii) comprises atleast one gene encoding an ATP binding cassette transporter; or iii)lacks at least one gene encoding a DNA binding response regulator or aphosphoglycerate kinase, and b. a pharmaceutically acceptable excipientor biological stabilizer.
 14. The method of claim 13, wherein the skindisorder or condition comprises acne, eczema, seborrheic dermatitis,psoriasis, or rosacea, or a combination thereof.
 15. The method of claim13, wherein the health-associated Propionibacterium acnes microbe hasbeen engineered or selected to at least one gene encoding thedeoxyribose operon repressor and the type II lipase.
 16. (canceled) 17.The method of claim 13, wherein the health-associated Propionibacteriumacnes microbe comprises an RT1 or RT2 ribotype.
 18. The method of claim13, wherein the health-associated Propionibacterium acnes microbe doesnot comprise an RT6 ribotype.
 19. (canceled)
 20. The method of claim 13,wherein the health-associated Propionibacterium acnes microbe comprisesa mixture of two or more different ribotypes.
 21. The method of claim13, wherein the health-associated Propionibacterium acnes microbecomprises an HP3A11 strain, an HP3B4 strain, an HP4G1 strain, or anHP5G4 strain.
 22. The method of claim 13, wherein the pharmaceuticalprobiotic composition comprises an additional strain of bacteria,wherein the additional strain comprises Propionibacterium avidum,Propionibacterium acnes subsp. defendens, or Propionibacteriumgranulosum.
 23. A pharmaceutical probiotic composition comprising: a. afirst therapeutically effective amount of a first health-associatedPropionibacterium acnes microbe, wherein the first health-associatedPropionibacterium acnes microbe is characterized by at least one of thefollowing: i) comprises at least one gene encoding at least one of adeoxyribose operon repressor and a type II lipase, and less than about10% pIMPLE plasmid; ii) comprises at least one gene encoding an ATPbinding cassette transporter; or iii) lacks at least one gene encoding aDNA binding response regulator or a phosphoglycerate kinase; b. a secondtherapeutically effective amount of a second health-associated microbe;and c. a pharmaceutically acceptable excipient or biological stabilizer.24. The pharmaceutical probiotic composition of claim 23, wherein thesecond health-associated microbe is a strain of bacteria comprising P.acnes, P. granulosum, P. acnes subsp. defendens or P. avidum.
 25. Thepharmaceutical probiotic composition of claim 23, wherein the secondhealth-associated microbe is characterized by at least one of thefollowing: a) comprises at least one gene encoding at least one of adeoxyribose operon repressor and a type II lipase, and less than about10% pIMPLE plasmid; b) comprises at least one gene encoding an ATPbinding cassette transporter; or c) lacks at least one gene encoding aDNA binding response regulator or a phosphoglycerate kinase. 26.(canceled)
 27. The pharmaceutical probiotic composition of claim 23,wherein the first health-associated Propionibacterium acnes microbe orthe second health-associated microbe comprises an isolated or purifiedstrain of bacteria. 28-30. (canceled)